title: X-radiation (XR) sensitive HCT116-CloneK: XR at 0 and 4 Gy

status: Public on Dec 08 2003

city: Ottawa

first: Felix

middle: M.

last: Mesak

state: ON

address: 503 Smyth Rd. 3rd Floor

department: Centre for Cancer Therapeutics

country: Canada

institute: Ottawa Regional Cancer Centre

summary:
cDNA microarray study of X-radiation (XR) sensitive HCT116-CloneK cells without XR, 10 minutes, 6 hours, or 24 hours after XR at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Keywords: time-course

middle: M

first: Cheng

middle: E

last: Ng

first: Wei

middle: L

last: Tan

first: Sami

middle: S

last: Qutob


title: Cervical Cancer

status: Public on Sep 12 2003

city: Piscataway

first: Khew-Voon

last: Chin

state: NJ

address: 164 Frelinghuysen Road

department: Chemical Biology

country: USA

institute: Ernest Mario School of Pharmacy, Rutgers University

summary:
Expression profiles in normal and cancerous cervix tissue samples
Keywords: other

first: Zachariah

last: Selvanayagam

first: Ragini

last: Vittal


title: Unirradiated HCT116-CloneK cells

summary:
cDNA microarray study of unirradiated X-radiation (XR) sensitive HCT116-CloneK cells versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Keywords: repeat sample


title: HCT116-CloneK cells 24 hours after XR treatment at 4 Gy

summary:
cDNA microarray study of X-radiation (XR) sensitive HCT116-CloneK cells 24 hours after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Keywords: repeat sample


title: HCT116-CloneK cells 10 minutes after XR treatment at 4 Gy

summary:
cDNA microarray study of X-radiation (XR) sensitive HCT116-CloneK cells 10 minutes after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Keywords: repeat sample


title: Bacillus cereus strain 31673

status: Public on Oct 28 2004

city: Rockville

first: David

last: Rasko

state: MD

address: 9712 Medical Center Drive

department: Microbial Genomics

institute: The Institute for Genomic Research

summary:
Comparative Genomic Hybridization.
Analysis of genomic content of closely related Bacillus species.
Refer to individual records for strain information.
Refer to platform and individual sample records for experimental protocols.
Keywords: other

sample_organism:
Bacillus cereus
Bacillus anthracis str. Ames

first: Tim

middle: D

last: Read

first: S

middle: N

last: Peterson

first: D

middle: A

first: J

last: Ravel

first: R

middle: Z

last: Cer

last: Rilstone

first: M

last: Wu

first: C

last: Fraser


title: V1 variant vs. V26 variant

status: Public on Mar 03 2004

city: Guelph

first: John

last: Nash

address: 110 Stone Road West

department: Laboratory for Foodborne Zoonoses

institute: Public Health Agency of Canada

summary:
Competitive hybridization of V1 variant versus V26 variant of genome sequenced C. jejuni strain 11168
Keywords: repeat sample

first: Catherine

last: Carrillo

first: Eduardo

last: Taboada

middle: H


title: V1 vs V1 FliA knockout

summary:
Competive hybridization of V1 variant of genome sequenced C. jejuni strain 11168 versus V1 variant in which fliA gene encoding sigma 28 has been disrupted
Keywords: repeat sample

first: Wendy

last: Findlay


title: HCT116-CloneK cells 6 hours after XR treatment at 4 Gy

first: Felix

last: Mesak

summary:
cDNA microarray study of X-radiation (XR) sensitive HCT116-CloneK cells six hours after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Keywords: repeat sample

first: Cheng

last: Ng

first: Wei

last: Tan


title: Loblolly pine - Juvenile vs Mature

status: Public on Aug 11 2003

city: Athens

first: Jeffrey

last: Dean

state: GA

department: Warnell School of Forest Resources

institute: University of Georgia

summary:
Phase transition in wood formation.
Keywords: repeat sample

first: Walter

middle: W

last: Lorenz

middle: F

first: W. Walter


title: T3,DITPA and CGS

status: Public on Aug 23 2003

city: Tucson

first: Niranjan

last: Maitra

state: AZ

address: 1501 North Campbell Avenue

department: Sarver Heart Center

institute: University of Arizona

summary:
Rat ventricular cardiomyocytes were prepared from 18 day old fetus. Approximately 6 million cells were plated on 100 mm culture plate. The serum used in the medium was depleted from thyroid hormone by passing through anion exchange resin column. After 48 hours of growth with 70% confluency, cells were exposed to either T3, DITPA or CGS for another 48 hours before harvesting. Final concentrations of T3, DITPA and CGS in the medium were 6nM, 218nM and 1nM respectively.

RNA was prepared from cells with Triazol. Twenty micrograms of total RNA was reverse transcribed and labeled with Alexa Fluor 546 and 647. Labeled probes were hybridized with Qiagen's rat unigene oligo library. After 2 low and 1 high stringency washes Prolong antifade was added to the slides to prevent bleaching effect. Slides were scanned in Array Worx scanner with dual wave length.

The data ratio was normalized using a location and intensity dependent Lowess formula.
Keywords: equivalent probe


title: Inflammatory gene profiles in human gastric mucosa

status: Public on Jan 07 2004

city: Stockholm

first: Qiang

last: Pan-Hammarström

address: F79, Huddinge Hospital

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

summary:
Helicobacter pylori (H. pylori) infection is associated with an inflammatory response in the gastric mucosa, ultimately leading to cellular hyperproliferation and malignant transformation. Hitherto, only expression of a single gene, or a limited number of genes, has been investigated in infected patients. Thus, the impact of H. pylori on the expression of a broad set of genes has not yet been analyzed. cDNA arrays were therefore used to establish the global pattern of gene expression in gastric tissue of healthy subjects and of H. pylori infected patients. Two main gene expression profiles were identified based on cluster analysis. The data obtained suggest a strong involvement of selected Toll-like receptors (TLRs)3, adhesion molecules, chemokines, and interleukins in the mucosal response. This pattern is clearly different from that observed using gastric epithelial cell lines infected in vitro with H. pylori. The genotype of the bacteria (presence of genes encoding CagA, VacA and BabA) was analyzed by PCR and shown to be associated with different expression profiles. The presence of a
Keywords = H. pylori
Keywords = gastric inflammation
Keywords = cytokines
Keywords: parallel sample

first: Sicheng

last: Wen


title: Inflammatory bladder response

status: Public on Aug 15 2003

city: Oklahoma City

first: Ricardo

last: Saban

state: OK

institute: University of Oklahoma Health Sciences Center

summary:
Bladders examined at 1, 4 and 24 hours after lipopolysaccharide, substance P or ovalbumin challenge.
Keywords: other

first: Igor

last: Dozmorov

first: Marcia

middle: R

first: Nicholas

last: Knowlton

first: Michael

last: Centola


title: V1 vs V1 FlhA knockout

first: John

summary:
Competitive hybridization of V1 variant of genome sequenced C. jejuni strain 11168 versus V1 variant in which flhA gene has been disrupted.
Keywords: repeat sample

first: Catherine


title: OA

status: Public on Nov 30 2003

city: Paris

first: El Houdaigui

last: Fatiha

department: Immunology Department

country: France

institute: Institut Cochin

summary:
patients affected by osteoarthritis
Keywords: repeat sample


title: BLI_maternal

status: Public on Nov 14 2003

city: Tsukuba City, Ibaraki

first: Chandana

last: Herath

address: Ikenodai 2

department: Development Biology

country: Japan

institute: National Institute of Agrobiological Sciences

summary:
The objective of the present study was to use our own fabricated bovine liver cDNA microarray to profile genome-wide expression patterns of genes in the liver of cow throughout pregnancy. Ten-microgram of pooled liver total RNA obtained from nonpregnant cycling cows was reverse transcribed in the presence of cyanine-3-fluorescent dye (Cy3)-conjugated dUTP (Amersham Pharmacia Biotech) by using Superscript II reverse transcriptase (Life Technologies, Rockville, MD) to yield Cy3 fluorescence-labeled control cDNA probe. Similarly, liver total RNA obtained from cows on days 19, 27, 49, 58, 150 and 245 of pregnancy was separately reverse transcribed in the presence of Cy5-conjugated dUTP by using Superscript II reverse transcriptase to yield Cy5 fluorescence-labeled test cDNA probe. After a 2-h reverse transcription reaction at 42oC, RNA was degraded by addition of 1.5 µl of an alkaline solution (1N NaOH / 20 mM EDTA), and neutralized by addition of 1.5 µl 1N HCl. The labeled control cDNA probe and test cDNA probe were then mixed and washed by centrifugation with TE (Tris-EDTA, pH 7.0) first and then with TE, 20 µg Salmon sperm DNA, 20 µg polyA and 20 µg yeast RNA in a Microcon YM-30 column (Millipore, Bedford, MA). The concentrated probe mix was adjusted with TE to a volume of 24.8 µl, denatured at 100oC for 2 min, spun for a few min and made to a final hybridization volume of 31 µl with 5.27 µl 20XSSC and 0.93 µl 10% SDS and kept at room temperature until used. Before hybridization, microarray glass slides were immersed in 0.2% SDS for 2 min followed by two washes each 2 min in autoclaved Milli Q water, and subjected to blocking in 180 ml of Methyl Pyrrolidinone (Aldrich) containing 2.7 g Succinic Anhydride (WAKO, Japan) and 15.3 ml 1M Boric acid (pH 8.0) solution for 20 min. Slides were then washed with autoclaved Milli Q water, and the spotted cDNA targets (microarray) were denatured in boiling water for 2 min. The slides were dehydrated in 100% ethanol for 2 min and air dried by spinning at a low speed. The mixture of labeled probes, for example, the control (Cy3) and test (Cy5), were then applied to the microarray, placed a cover slip carefully and incubated at 65oC for 14 – 16 h in a custom slide chamber with humidity maintained by a small reservoir of 3 x SSC. In addition, 3 - 6 µl of 3 x SSC was spotted at each corner of the slide, as far away from the array as possible. After incubation for 14 – 16 h at 65oC, the slides were washed in 2 x SSC / 0.03% SDS for 2 min, followed by washing in 2 x SSC, 1 x SSC and 0.2 x SSC, each for 2 min with gentle agitation, and air dried by spinning at a low speed. All hybridizations were performed in duplicate except those of days 19 and 27, where no reverse labeling was done. In addition, day 245 of pregnancy had three samples hybridized with two of them being labeled using the same dye combination and the other is reverse labeled. In the reverse labeling procedure, for example, the control liver cDNA and test liver cDNA, which had been first labeled with fluorescent dyes Cy3 and Cy5, respectively, were then labeled with Cy5 and Cy3, respectively. The microarray hybridization images were immediately scanned by GenePix 4000B (Axon Instrument, Union City, CA). The images acquired by scan were analyzed by GenePix Pro 4.0 software. The absolute feature (microarray spot) and background intensity of Cy3 and Cy5 for each feature on the array was obtained for the hybridized images. The local background intensity of each spot was smoothed by the local weight regression smoother (lowess smoother) and subtracted from feature intensity data. The subtracted intensity data were subjected to non-parametric regression and local variance normalization. The non-parametric regression can reduce intensity-depended biases. Compared with the linear regression, the accuracy is improved, if the points in scatter plot of Cy3 vs. Cy5 were not distributed around the straight line. The local variance normalization controls the noise (background) in the raw data to a greater extent where the normalized data, in many cases, did not show significant fold-differences in comparison with background-subtracted raw intensity ratios, which frequently displayed higher fold-differences. Thus, the variance method that we employed to bovine liver array data has produced much reliable normalized ratios. To group liver genes with similar expression patterns throughout bovine pregnancy, two clustering algorithm were employed. The hierarchical clustering algorithm was performed using the software, Cluster 3.0, created and made freely available by Dr. Michiel de Hoon (http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm) based on the original version written by Dr. Michael Eisen (http://rana.lbl.gov/), and the software TreeView (http://rana.lbl.gov/). For hierarchical clustering, genes with either 2 or more than 2-fold induction or 2 or more than 2-fold repression at least at one point of the sampling period were selected. All ratio values were log transformed (base 2) to treat inductions or repressions of identical magnitude as numerically equal but with opposite sign, and subjected to centroid linkage clustering. Self-Organizing Maps (SOMs) algorithm was performed using the software GeneCluster 2 made freely available by Whitehead Institute Center for Genome Research (http://www-genome.wi.mit.edu/cancer/software/genecluster2/gc2.html). The SOMs were performed on the present data to better visualization of clusters of genes with their expression patterns plotted on an x-y axis. For SOMs, genes with either 1.5-fold (and above) induction or 1.5-fold (and above) repression at least at one point of the sampling period were selected. The minimum fold difference i.e., 1.5-fold, chosen for the analyses in the present study was based on the calculation that the technical variation contributing to the expression level of each individual gene due either to different labeling efficiencies of cyanine dyes or labeling procedure or both, was found to be within the range of 1.41-fold induction or repression. Therefore, either the induction or the repression of a particular gene by 1.5-fold or above was considered significant.
Keywords = differential liver gene expression
Keywords = bovine pregnancy
Keywords = hierarchical clustering
Keywords = self-organizing maps
Keywords: time-course

middle: B

first: Satoshi

last: Shiojima

first: Hiroko

last: Ishiwata

first: Susumu

last: Katsuma

first: Tadashi

last: Kadowaki

first: Koichi

last: Ushizawa

first: Kei

last: Imai

first: Toru

last: Takahashi

first: Akira

last: Hirasawa

first: Gozoh

last: Tsujimoto

first: Kazuyoshi

last: Hashizume

last: Satoshi


title: Control vs. AngII Infusion

status: Public on Oct 20 2003

city: Boston

first: Faina

last: Schwartz

state: MA

address: 700 Albany Street,W508

department: Medicine, Hypertension Section

institute: Boston University School of Medicine

summary:
The genetic background of mice used in this study is mainly C57BL/6J with a small contribution from 129/Sv and DBA/2J strains. Male littermates were received continuous administration of AngII for 7 days at 0.9ug/hour. On day 7 of AngII infusion, the blood pressure of infused mice was (mmHg, mean ± SD) 156 ± 1, while the control littermates remained normotensive (106 ± 9).
Keywords: other


title: Cancer Genome Anatomy Project (CGAP) Human LongSAGE

city: Bethesda

first: Cancer Genome Anatomy Project

last: CGAP

department: Cancer Genome Anatomy Project

institute: National Cancer Institute

summary:
This series represents the Cancer Genome Anatomy Project SAGE library collection.  Libraries contained herein were either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.

SAGE libraries are named according to the following convention:
* SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2
* Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.

overall_design: 88 libraries

first: R

last: Strausberg

first: D

last: Gerhard

first: Gregory

middle: J

last: Riggins


title: SARS coronavirus series

status: Public on Oct 19 2003

city: San Francisco

first: Joe

last: DeRisi

state: CA

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary:
Set of microarray experiments used to identify an unknown coronavirus in a viral culture derived from a patient with SARS. March 2003.
Keywords = SARS
Keywords = coronavirus
Keywords = viral discovery
Keywords = viruses
Keywords = respiratory infection
Keywords: repeat sample

sample_organism:
Homo sapiens
Viruses

first: David

last: Wang

first: Anatoly

last: Urisman

first: Yu-Tsueng

last: Liu

first: Joseph


title: In vivo screen of Francisella tularensis subsp. novicida mutants in sequence defined transposon library

status: Public on Dec 31 2008

city: Seattle

first: Allison

last: Mitchell

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson CRC

summary:
We used an inhalation mouse model of infection to query a collection of 2149 mutants in a Francisella tularensis subsp. novicida background for genes required for growth, survival and systemic dissemination. A microarray-based genome-wide negative selection screen (Microarray tracking of transposon mutants = MATT) allowed us to monitor the behavior of transposon insertions in 1371 unique genes.  Interestingly most of these genes persisted in lung and colonized liver and spleen. We found 44 (35%) genes negatively selected in lung and 81 (65%) genes negatively selected in liver and/or spleen. If negative selection in lung occurred, the attenuated mutants in general persisted at 24h after infection, disseminated to liver and/or spleen and appeared to be lost in lung after 48 to 72h of infection. These genes with a strong phenotype in lung but also potential for dissemination might be attractive vaccine or drug candidates.
Keywords: Genome-Wide Negative Selection Screen

overall_design:
185 arrays, no duplicates/replicates
Filtered data (per organ/timepoint) provided as a supplementary file

first: Petra

last: Kraemer

first: Nina

last: Salama


title: RA

first: El Houdaigui

last: Fatiha

summary:
patients affected by rheumatoid arthritis
Keywords: repeat sample


title: Effect of high fat and low fat diet on liver expression

status: Public on Jul 31 2004

city: Cambridge

first: Jatin

last: Misra

institute: MIT

summary:
Timecourse analysis of the effect high fat  and low fat diets have on liver gene expression.  C57 and AJ strains examined at 0, 1, 3, 4, 5 ,6, 7, 8, 9, 10 and 11 weeks.
Keywords: other

first: Ilias

last: Alevizos

first: Greg

last: Stephanopoulos


title: Identification of new and unpredicted full length Arabidopsis genes

status: Public on Oct 30 2003

city: La Jolla

first: Jun

last: Lim

address: 10010 N. Torrey Pines Rd.

department: PBIO-E

institute: The Salk Institute for Biological Studies

type: Expression profiling by genome tiling array

summary:
Examination of cRNA from Arabidopsis flowers, roots and suspension cell culture using custom high-density Affymetrix genome tiling arrays in order to identify new and unpredicted genes.
Keywords: other

first: Huaming

last: Chen

first: Paul

last: Shinn

first: Christopher

last: Kim

first: Rosa

last: Cheuk

last: Dale

first: Curtis

last: Palm

first: Audrey

last: Southwick

first: Kayoko

last: Yamada

first: Hank

middle: C

last: Yu

first: Ronald

last: Davis

first: Athanasios

last: Theologis

last: Ecker


title: Identification of new full length Arabidopsis genes - pilot arrays

city: Albany

first: Atsunari

last: Tsuchisaka

address: 800 Buchanan St.

department: Plant Gene Expression Center

institute: University of California, Berkeley / USDA

summary:
Identification of new and unpredicted full length Arabidopsis genes.

Examination of cRNA prepared from  Arabidopsis thaliana ecotype Columbia light grown 7-day old seedlings, light grown 7-day old seedlings treated at 4 degrees C for 24hrs, and etiolated 7-day old seedlings using pilot genome tiling arrays.

Total RNA was isolated from seedlings with the TRIzol reagent procedure of Invitrogen, then poly(A)+ RNA was purified with Qiagen oligotex. One microgram poly(A)+ RNA was converted into ds-cDNA using T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions using ENZO labeling kit, fragmented and then 20 micrograms of fragmented cRNA were hybridized to the arrays according to Affymetrix instructions.
Keywords: other

first: Joseph

last: Wu


title: Phopshate starvation

status: Public on Aug 22 2003

first: Dennis

last: Wykoff

department: Biochemistry

institute: UCSF

summary:
Two arrays of phopshate starvation.  PHO5 spot was not good with some arrays, and so was quantitated on other arrays
Keywords: equivalent probe

first: Mike

last: Springer

first: Erin

last: O'Shea

first: Nicole

last: Miller


title: Phosphate metabolism in Saccharomyces cerevisiae

status: Public on Aug 29 2003

summary:
Investigation of Saccharomyces cerevisiae phosphate metabolism. Cells starved for phosphate, cells grown with intermediate and high phosphate concentrations, and PHO4 mutant cells examined.
Keywords: other


title: Acute myeloid leukemia study

status: Public on Apr 15 2004

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

summary:
Acute myeloid leukemia study.

Supplementary Table 1: Clinical, morphological, cytogenetic and molecular
genetic information on 116 AML patient samples.

Supplementary Table 2: Summary of the distribution of clinical and molecular
genetic characteristics within the AML sample set.

Supplementary Table 3: Fluorescence ratios of the 6,283 well-measured and
variably-expressed genes.

Supplementary Table 4: Clinical and laboratory characteristics of normal
karyotype predominant subtypes I and II.

Supplementary Table 5: Supervised analysis of group-specific gene expression
signatures.

Supplementary Table 6: Gene-expression outcome class predictor.

Supplementary Table 7: Multivariate proportional hazards analysis.
Keywords: other

first: L

last: Bullinger

first: K

last: Dohner

first: E

last: Bair

first: S

last: Frohling

first: R

last: Schlenk

last: Tibshirani

first: H

first: J


title: Identification of new full length Arabidopsis genes - whole genome arrays

summary:
Identification of new and unpredicted full length Arabidopsis genes.

Examination of cRNA prepared from Arabidopsis thaliana ecotype Columbia light grown 7-day old seedlings using whole genome tiling arrays.
Keywords: other

first: Kayoko

last: Yamada

first: Audrey

last: Southwick

last: Dale

first: Curtis

last: Palm

first: Hank

first: Huaming

last: Chen

first: Rosa

last: Cheuk

first: Christopher

last: Kim

first: Jun

last: Lim

first: Paul

last: Shinn


title: Endophyte-infected diet alters gene expression in heifer luteal tissue

status: Public on Oct 27 2003

city: Carbondale

first: M.

middle: Javed

last: Iqbal

state: IL

address: 176 Ag. Building, MC 4415

department: Animal Sci, Food & Nutrition + Plant, Soil & General Agriculture

institute: Southern Illinois University at Carbondale

summary:
Gene expression analysis in heifer luteal tissue by interspecies microarray analysis.
Post-pubertal heifers were fed diets containing endophyte free fescue seed (EF), endophyte infected fescue seed (EI) or EI seed supplemented with 1.44 mg domperidone/kg body weight (EID). One heifer from each treatment group was slaughtered at a local abattoir 11-14 days after ovulation (EF = 11d, EI = 14d and EID = 14d ) and used for this study. Ovaries were collected and shipped at room temperature to the laboratory.  Approximately 3 mm3 samples of luteal tissue were placed in cryovials and frozen at -80°C until processed.
One 3 mm3 sample each for the EI and EID treatments and two samples for the EF treatment were ground to a fine powder in liquid N and total RNA was extracted using the RNeasy® Mini Kit (Qiagen, Valencia, CA).  Quality and quantity of RNA was determined by gel electrophoresis and spectrophotometry.
Five µg of total RNA was converted to cDNA and then biotin-labeled cRNA by linear amplification (CodeLink® Expression Bioarrays, Amersham Biosciences Corp, Piscataway, NJ, USA). Ten micrograms of labeled cRNA were hybridized to CodeLink UniSet Rat I Bioarray (Amersham Biosciences Corp, Piscataway, NJ, USA) by the Amersham Biosciences Facility.
Keywords: other

first: M

last: Jones


title: UV Radiation gene profiling in Maize Genotypes with Varying Flavonoid Content

status: Public on Aug 04 2003

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

summary:
Microarray hybridization was used to assess acclimation responses to four UV regimes by near isogenic Zea mays lines varying in flavonoid content.
Keywords: other

first: Virginia

last: Walbot


title: Flower development FRI/FLC

status: Public on Aug 06 2003

city: Tübingen

first: Markus

last: Schmid

address: Speemannstrasse 37-39

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Developmental Biology

summary:
Arabiposis plants with  conbinations of different FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) alleles grown in short days (9L:15D) for 30 days at 21°C, then shifted to long days (16L:8D).

Genotypes:
Columbia wild type (Col-0): fri FLC
Columbia with introgressed FRI from Sf-2: FRI FLC
Columbia with introgressed FRI and deleted FLC (flc-3): FRI flc
Columbia with deleted FLC (flc-3): fri flc

Time points:
0, 2, and 4 days after shift to long days
Keywords = flowering
Keywords: time-course

first: Detlef

last: Weigel

first: Jan

middle: U

last: Lohmann


title: Sepsis gene expression profiling: murine splenic compared with hepatic responses

status: Public on Jul 16 2003

city: St. Louis

first: Jason

middle: Matthew

last: Laramie

state: MO

address: 660 South Euclid Avenue

department: Surgery

institute: Washington University

summary:
The aim of this series of experiments was to gain experience in sepsis gene expression profiling in a well-accepted model of murine polymicrobial abdominal sepsis and begin characterizing (in the parlance of genomics) the sepsis "transcriptome." DESIGN: Prospective animal study. SETTING: University-based animal research facility.SUBJECTS C57BL/6 mice. INTERVENTIONS: After induction of general anesthesia, cecal ligation and puncture were performed to induce peritonitis and polymicrobial sepsis. The control group had sham laparotomy only. Three samples of spleen and liver were collected from septic and sham animals at 24 hrs after laparotomy. Changes in expression were measured for 588 annotated mouse genes by using a commercially available complementary DNA microarray kit. MEASUREMENTS AND MAIN RESULTS: Broad-scale gene expression profiles were characterized for septic liver and spleen and compared with sham controls. The analytical tools used included commercially available software packages and a novel analysis program. Very little overlap was observed in the septic gene expression profiles of these two organs. Most of the genes identified have previously been linked to regulation of the inflammatory response; importantly, however, some have not. In addition, hierarchical cluster analysis showed that cecal ligation and puncture at 24 hrs induced coordinate expression of genes that alter cell signaling and survival pathways in spleen, consistent with previously published reports of sepsis-induced splenocyte apoptosis. The current limitations of microarray analysis as reflected in these studies are also discussed. CONCLUSIONS: Microarray technology provides a powerful new tool for rapidly analyzing tissue-specific changes in gene expression induced by sepsis in animal models.
Keywords: other

first: J

middle: P

last: Cobb

middle: M

first: G

last: Stormo

last: Morrissey

first: W

last: Shannon

first: Y

last: Qiu

first: I

last: Karl

first: T

middle: G

last: Buchman

first: R

last: Hotchkiss


title: AtSeedlingRootMunitionResponses

status: Public on Jul 30 2003

city: Athens

first: Jeffrey

last: Dean

department: Warnell School of Forest Resources

institute: University of Georgia

summary:
Roots transcriptome responses 14-day old Arabidopsis seedlings grown submerged in MS medium and exposed to TNT or RDX.
Keywords = phytoremediation
Keywords = explosives
Keywords = TNT
Keywords = RDX
Keywords: parallel sample

overall_design: Complete experiment contains only three samples, including the control.

first: Drew R.

last: Ekman

last: Lorenz

first: Alan E.

last: Przybyla

first: N. Lee

last: Wolfe

first: Jeffrey F.D.


title: Eucalyptus grandis BC progeny

city: Gainesville

first: Matias

last: Kirst

state: FL

institute: University of Florida

summary:
The gene expression profiles of the differentiating xylem of 91 Eucalyptus grandis backcross individuals were characterized following a loop design (Churchill, G.A. Nat Genet. 2002 Dec;32 Suppl:490-5). In this design, RNA from genotype 1666 (labeled with Cy5) was hybridized with RNA from genotype 1667 (labeled with Cy3) on the first slide(GEO accession number GSM7637); the same genotype 1667 (now labeled with Cy5) was compared with genotype 1669 (Cy3) on the second slide (GSM7638), and so on. The loop was completed when genotype 1666 (Cy3) was contrasted to individual 1796 (Cy3) on slide GSM7727. Therefore, 91 individuals (genotypes) from the E. grandis backcross population were analyzed in two replicates, one with RNA labeled with Cy3 and the other with Cy5.
Keywords = Eucalyptus, xylem, microarray
Keywords: ordered

platform_organism:
Eucalyptus grandis
Eucalyptus tereticornis

first: Ron

last: Sederoff


title: Endothelial cell profiles

city: Palo Alto

first: Jennifer

last: King

department: Cardiovascular Medicine

summary:
Umbilical vein, lung microvascular, aortic and coronary artery endothelial cell profiles generated. Further characterization gained by comparison with other selected cell types.
Keywords: other


title: SAM PMN Parturition

status: Public on Jul 22 2003

city: East Lansing

first: Sally

last: Madsen

state: MI

address: B212 Anthony Hall

department: Animal Science

institute: Michigan State University

summary:
Bovine blood neutrophil RNA from 4 primiparous Holstein cows was collected on days -7, 0, 0.25, and 1 (relative to parturition on day 0).   RNA was pooled across the four animals at the independent time points to obtain the 20 ug necessary for use in a loop design.  RNA pools were separated into two 10 ug aliquots prior to cDNA synthesis and dye coupling in a loop design.  Each sample was labeled with Cy3 and Cy5 and run in paired hybridizations as follows: GSM8506 compaired day 0.25 and day -7, GSM8507 compaired day 1 and day 0, GSM8508 compaired day -7 and day 1, GSM8509 compaired day 0 and 0.25.  This pairing strategy was utilized to directly compare day -7 samples with days 0.25 and 1 samples because results from previous experiments suggested that the most pronounced differences in gene expression would occur between these days.
Keywords = microarray, cDNA, bovine, neutrophil, parturition
Keywords: time-course

first: Ling-Chu

last: Chang

first: Marie-Clare

last: Hickey

first: Guilherme

last: Rosa

first: Paul

last: Coussens

first: Jeanne

middle: L

last: Burton


title: Comparative molecular analysis of developing mouse forelimbs and hindlimbs

first: Elliott

last: Margulies

department: Genome Technology Branch

institute: National Human Genome Research Institute

summary:
The analysis of differentially expressed genes is a powerful approach to elucidate the genetic mechanisms underlying the morphological and evolutionary diversity among serially homologous structures, both within the same organism (e.g., hand vs. foot) and between different species (e.g., hand vs. wing). In the developing embryo, limb-specific expression of Pitx1, Tbx4, and Tbx5 regulates the determination of limb identity. However, numerous lines of evidence, including the fact that these three genes encode transcription factors, indicate that additional genes are involved in the Pitx1-Tbx hierarchy. To examine the molecular distinctions coded for by these factors, and to identify novel genes involved in the determination of limb identity, we have used Serial Analysis of Gene Expression (SAGE) to generate comprehensive gene expression profiles from intact, developing mouse forelimbs and hindlimbs. To minimize the extraction of erroneous SAGE tags from low-quality sequence data, we used a new algorithm to extract tags from -analyzed sequence data and obtained 68,406 and 68,450 SAGE tags from forelimb and hindlimb SAGE libraries, respectively. We also developed an improved method for determining the identity of SAGE tags that increases the specificity of and provides additional information about the confidence of the tag-UniGene cluster match. The most differentially expressed gene between our SAGE libraries was Pitx1. The differential expression of Tbx4, Tbx5, and several limb-specific Hox genes was also detected; however, their abundances in the SAGE libraries were low. Because numerous other tags were differentially expressed at this low level, we performed a 'virtual' subtraction with 362,344 tags from six additional nonlimb SAGE libraries to further refine this set of candidate genes. This subtraction reduced the number of candidate genes by 74%, yet preserved the previously identified regulators of limb identity. This study presents the gene expression complexity of the developing limb and identifies candidate genes involved in the regulation of limb identity. We propose that our computational tools and the overall strategy used here are broadly applicable to other SAGE-based studies in a variety of organisms.
Keywords: other

first: Sharon L

last: Kardia

last: Innis


status: Public on Nov 13 2003

first: Terrill

middle: K.

last: McClanahan

address: 901 California Avenue

department: Experimental Pathology & Pharmacology

institute: DNAX Research Inc.

summary:
Genes regulated by inflammatory cytokines in five primary endothelial cell types
Keywords: ordered

first: Theodore

last: Sana

first: Mary

last: Janatpour

first: Manjiri

last: Sathe

first: Leslie

last: McEvoy

middle: K


title: Alpha Thalassaemia Myelodysplasia Syndrome (ATMDS)

status: Public on Jun 06 2003

city: Oxford

first: Andrea

last: Pellagatti

address: John Radcliffe Hospital

department: NDCLS, RDM

country: United Kingdom

institute: University of Oxford

summary:
A 10K cDNA microarray was used to compare granulocyte RNA from one ATMDS patient to pooled granulocyte RNA from 7 healthy controls.
Keywords: repeat sample

first: Richard

last: Gibbons

first: Jacqueline

last: Boultwood

first: James

middle: S

last: Wainscoat

first: Douglas

last: Higgs


title: Effect of uniconazole-P on wt and pkl mutant germinating seeds

status: Public on Jul 07 2003

city: West Lafayette

last: Romero-Severson

state: IN

institute: Purdue University

summary:
Relative expression data from germinating seeds of Columbia (wt), the pkl mutant (pkl), Columbia plus uniconazole-P (Uwt) and the pkl-mutant plus uniconazole-P (Upkl). Each experimental condition (wt, pkl, Uwt and Upkl) has four true replicates for a total of 16 chips.
Keywords = CHD3
Keywords = chromatin remodeling factors
Keywords = developmental transition
Keywords = embryo
Keywords = seed germination
Keywords: other

first: S Jr

last: Dean Rider

first: J

middle: T

last: Henderson

first: R

middle: E

last: Jerome

first: H

last: Edenberg

last: Ogas


title: Extraocular muscle, expression changes in critical period (Porter lab)

city: Cleveland

first: Henry

middle: J.

last: Kaminski

state: OH

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

summary:
Evaluation of extraocular muscle (EOM) critical period by expression profiling in dark reared rat.  Data form part of publication: Investigative Ophthalmology and Visual Sciences 44: 3842-3855, 2003.
Keywords: other

first: Georgiana

last: Cheng

first: Michael

last: Mustari

first: Sangeeta

last: Khanna

first: John

middle: D

last: Porter


title: High temperature adapted coli expression

status: Public on Jul 14 2003

city: Irvine

first: Michelle

last: Riehle

institute: University of California Irvine

summary:
Analysis of gene expression of mid log phase cultures of Escherichia coli Ancestor strain, and high temperature evolved lines 42-1, 42-2 and 42-3.
Keywords: other


title: IC - Experiment 3

city: Baltimore

first: Susan

last: Keay

institute: University of Maryland, Baltimore

summary:
Cells from 6 different IC patients were run in parallel with cells from their 6 different matched controls.
Keywords: other


title: IC - Experiment 1

summary:
Normal bladder epithelial cell explant from a single normal control was treated with APF from a single IC patient or mock APF. Two different membranes were used.
Keywords: other


title: IC - Experiment 2

summary:
Normal bladder epithelial cell explants from 2 different normal controls were treated with APF from 2 different IC patients or mock APF from 2 different matched controls.
Keywords: other


title: New targets of Drosophila adenosine deaminase acting on RNA (dADAR)

first: Shuli

last: Xia

institute: Kennedy-Krieger Institute

summary:
The aim of this experiment is to identify new targets of Drosophila adenosine deaminase acting on RNA (dADAR) by enriching Inosine-containing mRNA (I-mRNA) from wild type (C-S) and dADAR mutant flies and then hybridization with Drosophila cDNA arrays.
Keywords: other

first: Jinghua

last: Yang

first: Yingjun

last: Su

first: Jiang

last: Qian

first: Enbo

last: Ma

first: Gabriel

last: Haddad


title: Effect of serotonergic hallucinogen in mouse somatosensory cortex

status: Public on Apr 29 2003

city: New York

first: Elisa

last: Wurmbach

state: NY

address: 1 Gustave L. Levy Place

department: Hematology/Oncology

institute: Mount Sinai School of Medicine

summary:
To investigate the gene program activated by serotonergic hallucinogens in mouse somatosensory cortex, the effects of the 5-HT2A agonist (±)2,5-dimethoxy 4-iodoamphetamine (DOI) on gene expression was studied. The 5-HT2A serotonin receptor is a member of the 5-HT2 receptor subfamily of G protein–coupled receptors. The 5-HT2A receptor is thought to modulate processes related to cognition, appetite, mood, anxiety, sleep, and sexual behavior. Abnormal function of this receptor has been implicated in neuropsychiatric disorders such as major depression and schizophrenia. In particular, the 5-HT2A receptor has been implicated in the modulation of the mechanisms related to psychosis. We compared gene response patterns in the somatosensory cortical brain area, which has a high density of 5-HT2A receptors and has been implicated in the action of hallucinogenic drugs. Mice (strain 129Sv) were injected with DOI (2 mg/kg or 10 mg/kg) or vehicle, animals were sacrificed after 1 h, and somatosensory cortex samples dissected on ice for RNA extraction. Seven independent microarray hybridizations from seven different DOI- or vehicle-treated mouse pairs were performed.
Keywords: other

first: Javier

last: González-Maeso

first: Tony

last: Yuen

first: Barbara

last: Ebersole

first: Alena

last: Lira

first: Jay

middle: A

last: Gingrich

first: Stuart

last: Sealfon


title: Mouse T helper cell clones

status: Public on Jun 12 2003

first: Steve

last: Cobbold

state: Oxfordshire

address: South Parks Road

department: Sir William Dunn School of Pathology

summary:
Regulatory T cells overexpress a subset of Th2 gene transcripts.  A comparison of murine CD4+ Th1, Th2 and Tr1/Treg clones with identical TCR specificity for the male transplantation antigen H-Y.
Keywords = T cell, Th1, Th2, Tr1, CD4, clone
Keywords: other

first: Diana

last: Zelenika

first: Elizabeth

last: Adams

last: Humm

first: Luis

last: Graca

first: Sara

last: Thompson

first: Herman

last: Waldmann

first: Chun-Yen

last: Lin


title: SAGE analysis of mouse brain regions

status: Public on Jul 10 2003

city: Gif-sur-Yvette Cedex

first: Michel

last: de Chaldée

department: Département de Biologie Joliot-Curie

institute: CEA Saclay

summary:
SAGE analysis of various brain regions from 8- to 12-week-old male C57BL/6 mice.
Keywords: other

first: M

last: de Chaldee

last: Gaillard

first: N

last: Bizat

first: J

last: Buhler

first: O

last: Manzoni

last: Bockaert

first: P

last: Hantraye

first: E

last: Brouillet

last: Elalouf


title: Porcine brain library whole brain vs whole brain

status: Public on Jun 13 2003

first: Steven

middle: Paul

last: Suchyta

address: B215 Anthony Hall

summary:
series of experiments assesing false positive and background of pig brain library (PBL) microarray
Keywords = porcine brain, pig brain
Keywords: repeat sample

first: William

last: Nobis

first: Xiaoning

last: Ren

first: Adroaldo

middle: J

last: Zanella

first: Paul

last: Coussens


title: Deletions_TETs_WTs

city: Toronto

first: Timothy

middle: Richard

last: Hughes

state: ON

address: 112 College St.

department: Banting and Best Department of Medical Research

institute: University of Toronto

summary:
Analysis of noncoding RNA processing phenotypes in mutant yeast strains, with isogenic wildtype strains as controls two-color microarrays, total RNA labeled directly with Alexa Ulysis 546 and 648 dyes, dye-swap, eight replicates of each oligo per slide, Lowess smoother, Hedge et al. 2002 protocols, see Peng, Robinson et al., 2003.
Keywords: other


title: CD4/CD25 subsets of mouse spleen

first: Steve

last: Cobbold

summary:
A comparison of CD4+CD25+ and CD4+CD25- splenic T cells.  Although both subsets have regulatory T cell activity in an induced transplantation tolerance model, the CD4+CD25+ subsets are apparently 10 fold enriched in regulatory T cells.  SAGE analysis is performed and compared both on resting and CD3 activated populations.
Keywords: other

first: Luis

last: Graca

last: Thompson

last: Lin

first: Elizabeth

last: Adams

last: Waldmann


title: DNA repair in Mycobacterium tuberculosis

status: Public on Apr 18 2003

city: Rockville

first: Helena

middle: I

last: Boshoff

state: MD

address: 12441 Parklawn Drive

department: LIG

institute: NIAID/ NIH

summary:
Molecular analysis of DNA repair mechanisms in Mycobacterium tuberculosis.  Bacteria exposed to mitomycin C, UV irradiation or hydrogen perxoxide treatment for up to 12 hours.
Keywords: repeat sample

first: H


title: Somatic cells in testes

status: Public on May 06 2003

city: Glasgow

first: Peter

middle: James

last: O'Shaughnessy

address: Bearsden Rd

department: Veterinary Preclinical Studies

institute: University of Glasgow Veterinary School

summary:
Gene expression profiles of somatic cells of fetal and adult testis.

To identify genes developmentally regulated in the somatic cells of the testis, serial analysis of gene expression (SAGE) has been used to generate gene expression profiles from these cells in the fetal and adult mouse. To avoid germ cell transcripts, a fetal SAGE library was generated from germ cell-free fetal Wv/Wv mice, and an adult SAGE library was generated from adult testes depleted of germ cells with busulfan. The combined SAGE libraries contained 147570 tags identifying 12976 unique transcripts. Of these transcripts, 3607 were present in only the fetal library and 3941 were present in only the adult library. Most of the abundant differentially expressed tags in the adult testis library were from characterized genes, whereas 3' rapid amplification of complementary ends was required to identify most differentially expressed tags in the fetal library. These fetal tags were mostly associated with uncharacterized UniGene clusters. These data provide a comprehensive and quantitative analysis of gene expression in the somatic cells of the fetal and adult testis (including unknown transcripts) and identify genes differentially expressed in these cells during testis development. These differentially regulated genes are likely to provide insight into mechanisms regulating testis function both during development and in the adult animal.
Keywords: other

first: L

last: Fleming

last: Baker

first: G

last: Jackson

last: Johnston


title: Natural variation in human gene expression assessed in lymphoblastoid cells

status: Public on Apr 22 2003

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary:
Lymphoblastoid cells from 35 unrelated individuals used to examined variation in gene expression.  Identified genes whose transcript levels differed greatly among unrelated individuals.
Keywords: other

first: V

last: Cheung

last: Conlin

first: T

last: Weber

first: M

last: Arcaro

first: K

middle: Y

last: Jen

first: R

last: Spielman


title: Bacillus_anthracis_CGH

status: Public on May 01 2003

first: David

last: Rasko

address: 9712 Medical Center Drive

department: Microbial Genomics

institute: The Institute for Genomic Research

summary:
Analysis of genomic content of closely related Bacillus species.
Refer to individual records for strain information.
Refer to platform and individual sample records for experimental protocols.
Keywords: other

sample_organism:
Bacillus anthracis
Bacillus cereus
Bacillus mycoides
Bacillus thuringiensis

first: Tim

last: Read

first: S

middle: N

last: Peterson

first: N

last: Tourasse

middle: W

last: Baillie

first: I

last: Paulsen

last: Nelson

last: Tettelin

first: D

last: Fouts

first: J

last: Eisen

middle: R

last: Gill

first: E

last: Holtzapple

first: Ole Andreas

last: Økstad

last: Helgason

last: Rilstone

last: Wu

middle: F

last: Kolonay

last: Beanan

last: Dodson

middle: M

last: Brinkac

last: Gwinn

last: DeBoy

last: Madpu

middle: C

last: Daugherty

first: A

last: Durkin

middle: H

last: Haft

first: W

last: Pop

last: Khouri

last: Radune

last: Benton

first: Y

last: Mahamoud

last: Jiang

last: Hance


title: Hypo-osmotic shock - ppt1 and wildtype

status: Public on Apr 15 2003

city: Stanford

first: Eran

last: Segal

address: Gates Building 1A

department: Computer Science

institute: Stanford University

summary:
Wild type and ppt1 mutant under hypo-osmotic shock.

Cultures were grown with 1M sorbitol for ~20 hours, cells were collected by centrifugation and resuspended in YPD at time zero. Samples were collected at 0, 7, 15, 30 and 60 minutes after transfer to YPD.

Experimental samples were used to generate Cy5-labeled cDNA probes, whereas mRNA reference pools extracted from cultures of the respective strains grown to early log phase under normal conditions, were used to generate Cy3-labeled cDNA probes.  Cy5- and Cy3-labeled probes were hybridized together to microarrays printed with PCR-amplified fragments, representing 6280 of the Saccharomyces cerevisiae ORFs.
Keywords: time-course

first: Michael

last: Shapira

first: Aviv

last: Regev

first: Dana

last: Pe'er

last: Botstein

first: Daphne

last: Koller

first: Nir

last: Friedman


title: Heat shock - kin82 mutant and wildtype

summary:
Wild type and kin82 mutant under heat shock.

Cells grown at 25°C were collected by centrifugation, resuspended in an equal volume of 37°C medium, and returned to 37°C for growth.  Samples were collected at 0, 5, 15, 30 and 60 minutes after transfer to 37°C.

Experimental samples were used to generate Cy5-labeled cDNA probes, whereas mRNA reference pools extracted from cultures of the respective strains grown to early log phase under normal conditions, were used to generate Cy3-labeled cDNA probes.  Cy5- and Cy3-labeled probes were hybridized together to microarrays printed with PCR-amplified fragments, representing 6280 of the Saccharomyces cerevisiae ORFs.
Keywords: time-course

first: David


title: Stationary phase - ypl230w mutant and wildtype

summary:
Wild type and ypl230w mutant under stationary phase.

Cultures were grown to OD600 of 0.27 (Ypl230w mutants) and 0.4 (congenic wild-type; DBY8778), at which point time zero samples were collected.  Samples were further collected at 2 (or 3), 5, 7, 9, and 24 hours.

Experimental samples were used to generate Cy5-labeled cDNA probes, whereas mRNA reference pools extracted from cultures of the respective strains grown to early log phase under normal conditions, were used to generate Cy3-labeled cDNA probes.  Cy5- and Cy3-labeled probes were hybridized together to microarrays printed with PCR-amplified fragments, representing 6280 of the Saccharomyces cerevisiae ORFs.
Keywords: time-course


title: Spleen vs Terbutaline Treated B cell

status: Public on Apr 14 2003

city: Pasadena

first: Sangdun

last: Choi

address: 1200 E. California Blvd

department: Biology

institute: California Institute of Technology

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Terbutaline labeled with Cy5- time course with repeats
Keywords: ordered

first: Rebecca

last: Hart

first: Mi Sook

last: Chang

first: Jong-Woo

last: Kim

first: Yun Anna

last: Cao

first: Sun Young

last: Lee

first: Angela

last: Alexander

first: Joella

last: Grossoehme

first: Zhen

last: Yan

first: Robert

last: Hsueh


title: Spleen vs Untreated, cultured B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells untreated and cultured, labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs Sphingosine-1-phosphate Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs Tumor necrosis factor-alpha Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Tumor necrosis factor-alpha labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs SDF1 alpha (Stromal cell derived factor-1) Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with SDF1 alpha (Stromal cell derived factor-1) labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with SLC (Secondary lymphoid-organ chemokine) labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs Prostaglandin E2 Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs NGF (Nerve Growth Factor) Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with NGF (Nerve Growth Factor) labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs MIP3-alpha Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs TGF-beta (transforming growth factor-beta) Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with TGF-beta (transforming growth factor-beta) labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs Neuropeptide Y Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Neuropeptide Y labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs Platelet activating factor Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Platelet activating factor labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs Lysophosphatidic Acid Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Lysophosphatidic Acid labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs Leukotriene B4 (LTB4) Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs Insulin-like growth factor 1 gamma Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Insulin-like growth factor 1 labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs IFN gamma Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Interferon-gamma (IFN gamma) labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs IL10 Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with IL10 labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs IL4 Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with IL4 labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs Lipopolysaccharide (LPS) Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Lipopolysaccharide (LPS) labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs IFN beta Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Interferon-beta (IFN beta) labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs GHRH Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Growth Hormone Release Hormone (GHRH) labeled with Cy5- time course with repeats
Keywords: ordered

first: Mi-Sook

first: Yun-Anna

first: Sun-Young


title: Spleen vs fMLP Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with fMLP labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs ELC Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with ELC labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs CpG-oligodeoxynucleotide Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with CpG-oligodeoxynucleotide labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs Dimaprit Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Dimaprit labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs CGS Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with CGS labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs CD27 Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with CD27 labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs CD40 Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with CD40 labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs BLC Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with BLC labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs 2-Methyl-thio-ATP Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with 2-Methyl-thio-ATP labeled with Cy5- time course with repeats
Keywords: ordered


title: Spleen vs Bombesin Treated B cell

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Bombesin labeled with Cy5- time course with repeats
Keywords: ordered


title: Ciprofibrate stimulated gene expression in rats

status: Public on Mar 31 2003

city: Trondheim

first: Fekadu

last: Yadetie

address: Olav Kyrres gt 3

department: Cancer Research and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

summary:
Samples and RNA preparation:
The series is composed of 4 hybridizations for analysis of differentially expressed genes in the liver of ciprofibrate dosed vs. control rats. Rats (200-250 g) were given (by gastric intubation) tap water (control group, n=5) or ciprofibrate (50 mg/kg body weight, once daily for 60 days, n=4). Liver total RNA extraction was performed first by ultracentrifugation on a cesium chloride cushion and then using TRIZOL Reagent (GIBCO BRL Life Technologies, New York, NY).
Labeling and hybridization:
One microgram of total RNA from the control pool (n=5), and from each ciprofibrate dosed rat was reverse transcribed and labeled with Cy3- and Cy5-attached dendrimer, respectively, using 3DNA Array Detection Submicro kit as described in the manufacturer's protocols  (Genisphere, Montvale, NJ). The labeling reactions were also spiked with exogenous control RNAs (Stratagene) at expected Cy5/Cy3 ratios of 1.0, 2.0, 3.0, 4.0, 5.0, 6.0,  0.5, 0.33, 0.25 and 0.125 for control spike 1, 2, 3, 4, 5, 6, 8, 9, 10 and 7, respectively.
The Cy3 and Cy5 labeled samples (combined volume 5 microliter) were mixed with 30 microliter of the hybridization solution containing 0.25 M NaPO4, 1 mM EDTA, 4.5% SDS, 1 x SSC, 2 x Denhardt's solution, 0.25 microliter antifade reagent (Genisphere) and 0.2 microgram mouse COT-1 DNA (GIBCO BRL Life Technologies), added onto the array and covered with 22 x 50mm cover slip. The array was assembled into humidified hybridization chamber (Corning) and hybridized at 65oC for 18 h by submerging in a water bath. Post-hybridization washes were done once in 2 x SSC, 0.2% SDS at 55oC for 15 min, then in 2 x SSC at room temperature for 15 min, and finally with 0.2 x SSC at room temperature for 15 min.
Scanning, image analysis and data processing:
Arrays were scanned at 10 micrometer resolution with a confocal laser scanner constructed in-house in collaboration with NEMKO (Trondheim, Norway) according to a prototype developed at NHGRI (http://www.nhgri.gov/DIR/LCG/15K(HTML/).
Microarray image analysis was done with MicroArray Suite software version 2.1 with globally normalization (Scanalytics, Inc., Fairfax VA). First, spots undetected (target intensity=1) in at least one array were excluded. Then, spots with signal intensity (averages of the 4 arrays) less than 300 in both channels were removed. The fluorescence intensity ratios (Cy5/Cy3) for genes measured from probes spotted in duplicate were averaged for each slide. Then, mean ratios of the 4 hybridizations were calculated for each gene, and differentially regulated genes were determined using 1.4 fold change cutoff values (1.4 for up-regulated or 0.7 for down-regulated genes).
Keywords: other

first: F

first: A

last: Laegreid

first: I

last: Bakke

first: W

last: Kusnierczyk

first: J

last: Komorowski

first: H

middle: L

last: Waldum

middle: K

last: Sandvik


title: Somatic embryogenesis

city: Urbana

first: Lila

middle: O.

last: Vodkin

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary:
Examination of cotyledons after 7, 14, 21 and 28 days on 40mg/L 2,4-D.
Keywords: other

first: Francoise

last: Thibaud-Nissen

first: Robin

middle: T

last: Shealy

first: Anupama

last: Khanna

middle: O


title: Spleen vs BAFF Treated B cell

first: Sangdun

last: Choi

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with BAFF labeled with Cy5- time course with repeats
Keywords: ordered

first: Rebecca

last: Hart

first: Mi Sook

last: Chang

first: Jong-Woo

last: Kim

first: Yun Anna

last: Cao

first: Sun Young

first: Angela

first: Joella


title: Cerebellum of Lurcher (Lc +/-) mouse.

status: Public on Mar 24 2003

city: Columbus

first: Julie

last: Besco

department: Pharmacology

institute: The Ohio State University

summary:
Analysis of gene expression in cerebellum of postnatal day 10 Lurcher (Lc +/-) mouse, compared to wild type littermate.
Keywords: other

first: B

middle: A

first: A

last: Frostholm

last: Rotter


title: Sperm storage mechanisms in poultry

status: Public on Mar 23 2003

city: Beltsville

first: Kurt

middle: A.

last: Zuelke

address: Bldg 200, Barc-EAST

institute: USDA ARS Animal and Natural Resources Institute

summary:
Turkey sperm lose viability within 8-18 h when stored as liquid semen using current methods and extenders. In contrast, turkey hens maintain viable, fertile sperm in their sperm storage tubules (SST) for 45 or more days following a single insemination. Our long-term objectives are to identify and characterize differentially expressed genes that may underlie this prolonged sperm storage and then use this information to develop improved methods for storing liquid turkey semen. We employed serial analysis of gene expression (SAGE) to compare gene expression patterns in turkey SST recovered from hens after artificial insemination (AI) with extended semen (sperm AI) or extender alone (control AI). We constructed two separate SAGE libraries with SST RNA obtained from sperm and control AI hens. We used these libraries to generate 95,325 ten-base pair SAGE tags. These 95,325 tags represented 27,430 unique genes. The sperm and control AI libraries contained 47,663 and 47,662 tags representing 18,030 and 19,101 putative unique transcripts, respectively. Approximately 1% of these putative unique genes were differentially expressed (P<0.05) between treatments. Tentative annotations were ascribed to the SAGE tag nucleotide sequences by comparing them against publicly available SAGE tag and cDNA sequence databases. Based on its SAGE tag nucleotide sequence, we cloned a partial turkey avidin cDNA and confirmed its up-regulation in the sperm AI SST. The bioinformatics and experimental procedures employed to clone turkey avidin and confirm its differential expression represent a useful paradigm for analyzing SAGE tag data from relatively uncharacterized model systems.
Keywords: other

first: K

first: E

last: Long

first: T

middle: S

last: Sonstegard

first: J

first: C

middle: P

last: Van Tassell


title: cDNA array 6800 genes (NIB) - HaCaT J10 3h - 0.5&2 Gy

status: Public on Mar 13 2003

city: Evry

first: Jerome

last: Lamartine

address: 2 rue Gaston Cremieux

department: Departement de Radiobiologie et Radiopathologie

institute: CEA

summary:
Huamn HaCaT keratinocytes were cultured to confluence (day10). Differentiated confluent cells were irradiated at 0.5 Gy or 2 Gy.
RNA from irradiated cells was compared to RNA from non-irradiated reference cells in a dye-swap hybridization procedure 3 h after irradiation.
Keywords = Human keratinocytes, gamma irradiation
Keywords: dose response

first: Xavier

last: Gidrol

first: Gilles

last: Waksman

first: Michèle

last: Martin


title: Spleen vs Liver - Oligo - Single

status: Public on Mar 07 2003

first: Sangdun

summary:
Spleen total RNA (Catalog #64044-1) and liver total RNA (Catalog #64042-1) were purchased from Clontech and used as the starting material. Spleen was labeled with Cyanine-3 (Green) while liver was labeled with Cyanine-5 (Red). cRNA was made by the single round amplification method.
Keywords: repeat sample

first: Yun Anna

first: Sun-Young

last: Lee

first: Jong-Woo

first: Mi Sook

first: Melvin

middle: I

last: Simon


title: cDNA array 2304 genes (OSPE) - HaCaT J10 3h - 0.5&2 Gy

status: Public on Mar 11 2003

summary:
Human HaCaT keratinocytes were cultured to confluence (day10).
Differentiated confluent cells were irradiated at 0.5 Gy or 2 Gy.
RNA from irradiated cells was compared to RNA from non-irradiated reference cells in a dye swap hybridization procedure 3 h after irradiation.
Keywords = Human keratinocytes, gamma irradiation
Keywords: dose response

last: Lemaitre


title: cDNA array 6800 genes (NIB) - HaCaT J10 24h - 0.5&2 Gy

status: Public on Mar 26 2003

summary:
Human HaCaT keratinocytes were cultured to confluence (day10). Differentiated confluent cells were irradiated at 0.5 Gy or 2 Gy.
RNA from irradiated cells was compared to RNA from non-irradiated reference cells in a dye-swap hybridization procedure 24 h after irradiation.
Keywords = human keratinocytes, gamma irrdiation
Keywords: dose response


title: cDNA array 2304 genes (OSPE) - HaCaT J10 24h - 0.5& 2 Gy

status: Public on Mar 25 2003

summary:
Human keratinocytes were cultured to confluence (day 10). Differentiated confluent cells were irradiated at 0.5 and 2 Gy. RNA from irradiated cells was compared to RNA from non-irradiated reference cells in a dye-swap procedure 24 h after irradiation.
Keywords = Human keratinocytes, gamma irradiation
Keywords: dose response


title: Spleen vs Anti-IgM Treated B cell

last: Choi

summary:
total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Anti-IgM labeled with Cy5- time course with repeats
Keywords: ordered

first: Rebecca

last: Hart

last: Chang

first: Sun Young

first: Angela

last: Alexander

first: Joella

last: Grossoehme

first: Zhen

last: Yan

first: Robert

last: Hsueh


title: MK-DG vs MK C+S-DG

status: Public on Feb 27 2003

summary:
MK: MK-801. Young male C57BL/6J mice received an injection of MK-801 (300 micro-g per g body weight). RNA from control mice were extracted 1hr, 2hr, 4hr, and 6hr after MK experimental mice received their last shock treatment.
MK C+S: MK-801 & Context + Shock: Young male C57BL/6J mice received an injection of MK-801 (300 micro-g per g body weight) 1 h prior to contextual fear conditioning that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted 1hr, 2hr, 4hr, and 6hr after the last shock treatment.
Keywords: time-course

first: Jonathan

last: Levenson

last: Cao

first: Kim

last: Worley

first: Hui

last: Zheng

first: David

last: Sweatt


title: Molecular profiling of human hepatocarcinogenesis

status: Public on Apr 03 2003

city: Bethesda

first: Xin

middle: Wei

last: Wang

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary:
Comparison of hepatocellular carcinoma with non-cancerous liver tissue.
Keywords: repeat sample


title: HaCaT keratinocytes day3 vs HaCaT keratinocytes day10

first: Jerome

last: Lamartine

summary:
The keratinocyte cell line HaCaT was cultured for three days (proliferation) or for ten days (differentiation).
RNA from cells at day3 was compared to RNA from cells at day10.
The microarray hybridizations were performed in dye-swap procedure : RNA from cells at day3 was labeled with Cy3 (GSM4674, GSM4675, GSM4682, GSM4683) and then with cy5 (GSM4680, GSM4681).
Keywords = cell density differentiation program in human keratinocytes
Keywords: repeat sample

first: Gilles

first: Xavier

last: Gidrol

first: Michèle

last: Martin

last: Waksman


title: MK-CA1 vs MK C+S-CA1

first: Sangdun

last: Choi

first: Sun-Young

last: Lee

first: Yun Anna

last: Simon


title: Lipopolysaccharide-stimulated neutrophils

status: Public on Mar 10 2003

city: Denver

first: K

last: Malcolm

state: CO

department: Department of Medicine

institute: National Jewish Medical and Research Center

summary:
Neutrophil gene transcription following lipopolysaccharide exposure.
Microarray analysis of lipopolysaccharide-treated human neutrophils.
Neutrophils respond to infection by degranulation, release of reactive oxygen intermediates, and secretion of chemokines and cytokines; however, activation of neutrophil transcriptional machinery has been little appreciated. Recent findings suggest that gene expression may represent an additional neutrophil function after exposure to lipopolysaccharide (LPS). We performed microarray gene expression analysis of 4,608 mostly nonredundant genes on LPS-stimulated human neutrophils. Analysis of three donors indicated some variability but also a high degree of reproducibility in gene expression. Twenty-eight verifiable, distinct genes were induced by 4 h of LPS treatment, and 13 genes were repressed. Genes other than cytokines and chemokines are regulated; interestingly, genes involved in cell growth regulation and survival, transcriptional regulation, and interferon response are among those induced, whereas genes involved in cytoskeletal regulation are predominantly repressed. In addition, we identified monocyte chemoattractant protein-1 as a novel LPS-regulated chemokine in neutrophils. Included in these lists are five clones with no defined function. These data suggest molecular mechanisms by which neutrophils respond to infection and indicate that the transcriptional potential of neutrophils is greater than previously thought.
Keywords: repeat sample

first: P

middle: G

last: Arndt

first: E

middle: J

last: Manos

first: D

last: Jones

first: G

last: Worthen


title: LT2_log_overnight_1

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary:
comparative hybridization of Typhimurium LT2 gDNA from logarithmic and stationary cultures on STv2
Keywords: repeat sample

first: Steffen

last: Porwollik

first: Jonathan

last: Frye

first: L

middle: D

last: Florea

first: Felisa

last: Blackmer


title: TY2_hydrogen_peroxide_2mM_RNA

status: Public on Mar 08 2003

summary:
Gene expression in Salmonella enterica sv Typhi TY2 after exposure to 2mM hydrogen peroxide
Keywords: time-course

sample_organism: Salmonella enterica subsp. enterica serovar Typhi


title: CT18_log_overnight_1

summary:
comparative hybridization of gDNA from logarithmic and stationary CT18 cultures on STv2
Keywords: repeat sample


title: CT18_LT2_STv2

summary:
comparative DNA hyb of CT18 and LT2 gDNA to the Salmonella chip STv2
Keywords: repeat sample


title: Sal-DG vs MK-DG

summary:
Sal: Saline. Young male C57BL/6J mice received an injection of saline (5 microL per g body weight). RNA from control mice were extracted 1hr, 2hr, 4hr, and 6hr after MK experimental mice received their last shock treatment.
MK: MK-801. Young male C57BL/6J mice received an injection of MK-801 (300 micro-g per g body weight). RNA from control mice were extracted 1hr, 2hr, 4hr, and 6hr after MK experimental mice received their last shock treatment.
Keywords: time-course

middle: M

last: Levenson

last: Cao

first: Kim

last: Worley

first: Hui

last: Zheng

first: Melvin

first: David

last: Sweatt


title: Sal-CA1 vs MK-CA1

first: Sangdun

last: Choi

last: Lee


status: Public on Jan 27 2003

city: Cambridge

first: Scott

last: Rifkin

address: 16 Divinity Ave

department: OEB

institute: Harvard University

summary:
Drosophila melanogaster OregonR blue gut larvae vs. white prepupae
Keywords: repeat sample

first: Junhyong

last: Kim

first: Kevin

last: White


summary:
Drosophila melanogaster Netherlands2 blue gut larvae vs. white prepupae
Keywords: repeat sample


summary:
Drosophila melanogaster Samarkand blue gut larvae vs. white prepupae
Keywords: repeat sample


summary:
Drosophila simulans blue gut larvae vs. white prepupae
Keywords: repeat sample


title: Differential expression of Aspergillus genes during the induction of aflatoxin biosynthesis

status: Public on Jan 15 2003

city: Raleigh

first: Ahmad

last: Fakhoury

state: NC

department: Plant Pathology

institute: North Carolina State University

summary:
Gene expression analysis of A. parasiticus grown under conditions conducive and nonconductive for aflatoxin production was evaluated using glass slide microarrays containing the 753 ESTs.

A complex regulatory network governs the biosynthesis of aflatoxin. While several genes involved in aflatoxin production are known, their action alone cannot account for its regulation. Arrays of clones from an Aspergillus flavus cDNA library and glass slide microarrays of ESTs were screened to identify additional genes. An initial screen of the cDNA clone arrays lead to the identification of 753 unique ESTs. Many showed sequence similarity to known metabolic and regulatory genes; however, no function could be ascribed to over 50% of the ESTs. Gene expression analysis of Aspergillus parasiticus grown under conditions conducive and non-conductive for aflatoxin production was evaluated using glass slide microarrays containing the 753 ESTs. Twenty-four genes were more highly expressed during aflatoxin biosynthesis and 18 genes were more highly expressed prior to aflatoxin biosynthesis. No predicted function could be ascribed to 18 of the 24 genes whose elevated expression was associated with aflatoxin biosynthesis.
Keywords = Aspergillus
Keywords = aflatoxin
Keywords: time-course

first: Gregory

middle: R

last: OBrian

first: Gary

last: Payne


state: MA

summary:
Drosophila melanogaster CantonS blue gut larvae vs. white prepupae
Keywords: repeat sample


title: Gene-expression profile comparisons distinguish seven organs of maize

status: Public on Jan 08 2003

city: Stanford University

first: Yangrae

last: Cho

state: CA

address: 385 Serra Mall

department: Biological Sciences

summary:
A maize array was fabricated with 5,376 unique expressed sequence tag (EST) clones sequenced from 4-day-old roots, immature ears and adult organ cDNA libraries. To elucidate organ relationships, relative mRNA levels were quantified by hybridization with embryos, three maize vegetative organs (leaf blades, leaf sheaths and roots) from multiple developmental stages, husk leaves and two types of floral organs (immature ears and silks).
Clustering analyses of the hybridization data suggest that maize utilizes both the PEPCK and NADP-ME C(4) photosynthetic routes as genes in these pathways are co-regulated. Husk RNA has a gene-expression profile more similar to floral organs than to vegetative leaves. Only 7% of the genes were highly organ specific, showing over a fourfold difference in at least one of 12 comparisons and 37% showed a two- to fourfold difference. The majority of genes were expressed in diverse organs with little difference in transcript levels. Cross-hybridization among closely related genes within multigene families could obscure tissue specificity. As a first step in elucidating individual gene-expression patterns, we show that 45-nucleotide oligo probes produce signal intensities and signal ratios comparable to PCR probes on the same matrix.
Gene-expression profile studies with cDNA microarrays provide a new molecular tool for defining plant organs and their relationships and for discovering new biological processes in silico. cDNA microarrays are insufficient for differentiating recently duplicated genes. Gene-specific oligo probes printed along with cDNA probes can query individual gene-expression profiles and gene families simultaneously.
Keywords: other

first: Y

first: J

last: Fernandes

first: S

middle: H

first: V

last: Walbot


title: Mammary tissue gene expression studies

status: Public on Feb 07 2003

city: East Lansing

first: Steven

middle: Paul

last: Suchyta

department: Animal Science

institute: Michigan State University

summary:
A series of experiments to establish a  bovine developing mammary gland gene expression signature, identify genes differentially expressed in bovine lactating mammary gland, and to establish the false positive rate of the BMAM microarray
Keywords = gene expression, differential expression, lactation, development, physiology, bovine, mammary, microarray, EST, cDNA
Keywords: repeat sample

first: Sue

last: Sipkovsky

first: Robert

last: Halgren

first: Paul

last: Coussens


title: Overexpression of the plant LAMMER kinase PK12

status: Public on Feb 05 2003

city: Rehovot

last: Fluhr

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

summary:
Comparison of plants that overexpress PK12 and non-transformed plants. Plants were grown for 10 days under long day conditions (GSM3816-GSM3819) or plants were grown for 21 days under long day conditions (GSM3820-GSM3823) . Hybridization was performed on arrays from Arabidopsis Keck Resource Lab Array (Yale University) containing 12K (GSM3816-GSM3819) or 9K (GSM3820-GSM3823)Arabidopsis ESTs. The 4 samples corresponding to each array represent 2 repetitions of 2 independent biological experiments.
Keywords = Alternative splicing
Keywords = phosphorylation
Keywords: equivalent probe

first: Sigal

last: Savaldi-Goldstein

first: Olga

last: Davydov

first: Dvora

last: Aviv


title: Embryo development of Medicago truncatula

status: Public on Nov 20 2002

city: Ardmore

first: Zeji

last: Du

state: OK

address: 2510 Sam Noble Parkway

department: Plant Biology Division

institute: Samuel Roberts Noble Foundation

summary:
Early stage of embryo development from leaf-derived embryogenic callus of M. truncatula.
Keywords: parallel sample

first: Angela

last: Scott

first: Gregary

last: May


title: Lager beer fermentation time course

status: Public on Sep 09 2002

city: Copenhagen Valby

first: Kjeld

last: Olesen

address: Gamle Carlsberg Vej 10

country: Denmark

institute: Carlsberg Research Laboratory

summary:
The dynamics of the Saccharomyces carlsbergensis brewing yeast transcriptome during a production scale lager beer fermentation.

The transcriptome of a lager brewing yeast (Saccharomyces carlsbergensis, syn. of S. pastorianus), was analysed at 12 different time points spanning a production-scale lager beer fermentation. Generally, the average expression rapidly increased and had a maximum value on day 2, then decreased as the sugar got consumed. Especially genes involved in protein and lipid biosynthesis or glycolysis were highly expressed during the beginning of the fermentation. Similarities as well as significant differences in expression profiles could be observed when comparing to a previous transcriptome analysis of a laboratory yeast grown in YPD. The regional distribution of various expression levels on the chromosomes appeared to be random or near-random and no reduction in expression near telomeres was observed.
Keywords: time-course

first: Troels

last: Felding

first: Claes

last: Gjermansen

first: Jorgen

last: Hansen


title: Proteomic view of the Plasmodium falciparum life cycle

status: Public on Dec 23 2002

city: La Jolla

first: Laurence

last: Florens

address: SR-11, 10550 North Torrey Pines Road

department: Department of Cell Biology

institute: The Scripps Research Institute

summary:
The completion of the Plasmodium falciparum clone 3D7 genome provides a basis on which to conduct comparative proteomics studies of this human pathogen. Here, we applied a high-throughput proteomics approach to identify new potential drug and vaccine targets and to better understand the biology of this complex protozoan parasite. We characterized four stages of the parasite life cycle (sporozoites, merozoites, trophozoites and gametocytes) by multidimensional protein identification technology. Functional profiling of over 2,400 proteins agreed with the physiology of each stage. Unexpectedly, the antigenically variant proteins of var and rif genes, defined as molecules on the surface of infected erythrocytes, were also largely expressed in sporozoites. The detection of chromosomal clusters encoding co-expressed proteins suggested a potential mechanism for controlling gene expression.
Keywords: ordered

first: L

first: M

last: Washburn

first: J

last: Raine

first: R

last: Anthony

last: Grainger

last: Haynes

middle: K

last: Moch

first: N

last: Muster

middle: B

last: Sacci

first: D

middle: L

last: Tabb

first: A

last: Witney

last: Wolters

first: Y

last: Wu

last: Gardner

last: Holder

middle: E

last: Sinden

last: Yates

last: Carucci


title: Heat shock experimental replicates

status: Public on Jan 21 2003

city: Tucson

first: Jennifer

last: Wilcox

state: AZ

department: EEB

institute: University of Arizona

summary:
Heat stress experiments imposed on Buchnera aphidicola within intact Schizaphis graminum hosts. NOTE: normalized values in GEO are NOT those derived from intensive analyses described in paper. Please see Wilcox et al. 2002 for description.
Keywords = reduced bacterial genome, stress response
Keywords: repeat sample

sample_organism: Buchnera aphidicola (Schizaphis graminum)

first: Helen

last: Dunbar

first: Russell

last: Wolfinger

first: Nancy

middle: A

last: Moran


title: Bovine Glomerular and Aortic Endothelial Cells

status: Public on Dec 10 2002

city: Bronx

first: Barbara

middle: Jutta

last: Ballermann

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

summary:
SAGE libraries were prepared from mRNA of cultured bovine glomerular and aortic endothelial cells. Cells both cell lines were positive for acetylated LDL uptake and vWF expression, and were proven to be free of non-endothelial cells.  Cultures were studied at passage 9-10. The cells were confluent, cultured in parallel, under identical conditions. Cells were plated on gelatin coated cell culture plastic in RPMI 1640 medium containing 10% FBS and streptomycin/penicillin. The last medium change was 48 hours prior to mRNA harvest.
Keywords = endothelial, glomerular, kidney, aorta,
Keywords: other

first: Guerkan

last: Sengolge

first: Wencheng

last: Luo


title: Antibody Arrays Figure 6 100X FCS

status: Public on Jun 27 2002

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions.
This study is described more fully in Haab, Dunham, and Brown, Genome Biology 2001 2(2): research0004.1-0004.13
Keywords: other

first: B

last: Haab

last: DunhaM

first: P

middle: O

last: Brown


title: Secreted and membrane-associated genes

summary:
Large-scale identification of secreted and membrane-associated gene products using DNA microarrays.
This study is described more fully in Diehn M et al.(2000) Nat Genet 25:58-62
Keywords: other

last: Diehn

last: Eisen

last: Botstein


title: DNA copy-number changes

summary:
Gene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome. With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation. CGH, however, has a limited ( approximately 20 Mb) mapping resolution, and higher-resolution techniques, such as fluorescence in situ hybridization (FISH), are prohibitively labour-intensive on a genomic scale. Array-based CGH, in which fluorescence ratios at arrayed DNA elements provide a locus-by-locus measure of DNA copy-number variation, represents another means of achieving increased mapping resolution. Published array CGH methods have relied on large genomic clone (for example BAC) array targets and have covered only a small fraction of the human genome. cDNAs representing over 30,000 radiation-hybrid (RH)-mapped human genes provide an alternative and readily available genomic resource for mapping DNA copy-number changes. Although cDNA microarrays have been used extensively to characterize variation in human gene expression, human genomic DNA is a far more complex mixture than the mRNA representation of human cells. Therefore, analysis of DNA copy-number variation using cDNA microarrays would require a sensitivity of detection an order of magnitude greater than has been routinely reported. We describe here a cDNA microarray-based CGH method, and its application to DNA copy-number variation analysis in breast cancer cell lines and tumours.
This study is described more fully in Pollack JR et al.(1999) Nat Genet 23:41-6
Keywords: other

last: Pollack

first: C

last: Perou

last: Alizadeh

last: Pergamenschikov

middle: F

last: Williams

first: S

middle: S

last: Jeffrey


title: Molecular portraits of human breast tumors

summary:
Set of 65 surgical specimens of human breast tumors from 42 different individuals, using complementary DNA microarrays representing 8,102 human genes. Gene expression variation patterns within this set provided a distinctive molecular portrait of each tumor. Twenty of the tumors were sampled twice, before and after a 16-week course of doxorubicin chemotherapy, and two tumors were paired with a lymph node metastasis from the same patient. Gene expression patterns in two tumor samples from the same individual were almost always more similar to each other than either was to any other sample.
This study is described more fully in Perou CM et al.(2000) Nature 406:747-52
Keywords: other

first: T

last: Sorlie

first: M

last: van de Rijn

last: Rees

first: J

middle: T

last: Ross

first: H

last: Johnsen

first: L

last: Akslen

first: O

last: Fluge

middle: X

last: Zhu

last: Lonning

last: Borresen-Dale


title: Antibody Arrays Figure 6 10X FCS

last: Stanford Microarray Database

last: Haab

middle: J

last: DunhaM

last: Brown


title: Serum stimulation of fibroblasts

summary:
The temporal program of gene expression during a model physiological response of human cells, the response of fibroblasts to serum, was explored with a complementary DNA microarray representing about 8600 different human genes. Genes could be clustered in groups on the basis of their temporal patterns of expression in this program. Many features of the transcriptional program appeared to be related to the physiology of wound repair suggesting that fibroblasts play a larger and richer role in this complex multicellular response than had previously been appreciated.
This study is described more fully in Iyer VR, et al. 1999. Science 283:83-7
Keywords: other

first: V

last: Iyer

last: Eisen

first: D

first: G

last: Schuler

last: Moore

middle: C

last: Lee

last: Trent

last: Staudt

last: Hudson

last: Boguski

last: Lashkari

last: Shalon

last: Botstein


title: Antibody Array Figures

summary:
Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions.
This study is described more fully in Haab, Dunham, and Brown, Genome Biology 2001 2(2): research0004.1-0004.13.
Keywords: other

last: Dunham


title: Serum stimulation of fibroblasts controls

last: Stanford Microarray Database

summary:
The transcriptional program in the response of human fibroblasts to serum control group.
This study is described more fully in Iyer VR, et al. 1999. Science 283:83-7
Keywords: other

last: Ross

middle: M


title: Mefloquine treatment of NG108 rat neuronal cells

status: Public on Nov 19 2002

city: Silver Spring

first: Geoffrey

last: Dow

address: Robert Grant Ave.

department: Division of Experimental Therapeutics, Building 503

institute: Walter Reed Army Institute of Research

summary:
This data series describes expression data for eight paired, control and treated cell cultures obtained on independent occasions. NG108 rat neuronal cell cultures were exposed to either 0.25% DMSO (control) or 4400 ng/ml mefloquine (treated) for two hours.
Validation:   Modulation of the following transcripts by mefloquine was confirmed by semi-quantitative RT-PCR:  U30186, X63594cds_g_at, X63594cds_at, X17163cds_s_at, rc_AI175959 and rc_AA945867 (unpaired, unequal variance, one tailed t-test, p < 0.05).
Keywords: other


title: mRNAs translated at eIF4F

summary:
Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Although most eukaryotic mRNAs need a functional cap binding complex eIF4F for efficient 5' end-dependent scanning to initiate translation, picornaviral, hepatitis C viral, and a few cellular RNAs have been shown to be translated by internal ribosome entry, a mechanism that can operate in the presence of low levels of functional eIF4F. To identify cellular mRNAs that can be translated when eIF4F is depleted or in low abundance and that, therefore, may contain internal ribosome entry sites, mRNAs that remained associated with polysomes were isolated from human cells after infection with poliovirus and were identified by using a cDNA microarray. Approximately 200 of the 7000 mRNAs analyzed remained associated with polysomes under these conditions. Among the gene products encoded by these polysome-associated mRNAs were immediate-early transcription factors, kinases, and phosphatases of the mitogen-activated protein kinase pathways and several protooncogenes, including c-myc and Pim-1. In addition, the mRNA encoding Cyr61, a secreted factor that can promote angiogenesis and tumor growth, was selectively mobilized into polysomes when eIF4F concentrations were reduced, although its overall abundance changed only slightly. Subsequent tests confirmed the presence of internal ribosome entry sites in the 5' noncoding regions of both Cyr61 and Pim-1 mRNAs. Overall, this study suggests that diverse mRNAs whose gene products have been implicated in a variety of stress responses, including inflammation, angiogenesis, and the response to serum, can use translational initiation mechanisms that require little or no intact cap binding protein complex eIF4F.
This study is described more fully in Johannes G et al.(1999) Proc Natl Acad Sci U S A 96:13118-23.
Keywords: other

last: Johannes

last: Carter

last: Brown

last: Sarnow


title: Antibody Arrays Figures 2, 4 and 6

last: Haab

last: DunhaM


title: Serum stimulation of fibroblasts experiment set

summary:
The transcriptional program in the response of human fibroblasts to serum. Serum was added to fibroblasts, and samples were taken.
This study is described more fully in Iyer VR, et al. 1999. Science 283:83-7
Keywords: time-course

middle: R

last: Iyer

last: Eisen

last: Schuler

last: Moore

last: Lee

last: Trent


title: Human mammary epithelium and breast cancer

summary:
Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. cDNA microarrays and a clustering algorithm were used to identify patterns of gene expression in human mammary epithelial cells growing in culture and in primary human breast tumors. Clusters of coexpressed genes identified through manipulations of mammary epithelial cells in vitro also showed consistent patterns of variation in expression among breast tumor samples. By using immunohistochemistry with antibodies against proteins encoded by a particular gene in a cluster, the identity of the cell type within the tumor specimen that contributed the observed gene expression pattern could be determined. Clusters of genes with coherent expression patterns in cultured cells and in the breast tumors samples could be related to specific features of biological variation among the samples. Two such clusters were found to have patterns that correlated with variation in cell proliferation rates and with activation of the IFN-regulated signal transduction pathway, respectively. Clusters of genes expressed by stromal cells and lymphocytes in the breast tumors also were identified in this analysis. These results support the feasibility and usefulness of this systematic approach to studying variation in gene expression patterns in human cancers as a means to dissect and classify solid tumors.
This study is described more fully in Perou CM, et al. 1999. Proc Natl Acad Sci USA 96:9212-7
Keywords: other

last: Perou

last: Jeffrey

last: van de Rijn

last: Rees

first: A

last: Pergamenschikov

last: Williams

last: Zhu

last: Lashkari

last: Shalon

last: Botstein


title: Human cancer cell lines

last: Stanford Microarray Database

summary:
We used cDNA microarrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute's screen for anti-cancer drugs. Classification of the cell lines based solely on the observed patterns of gene expression revealed a correspondence to the ostensible origins of the tumors from which the cell lines were derived. The consistent relationship between the gene expression patterns and the tissue of origin allowed us to recognize outliers whose previous classification appeared incorrect. Specific features of the gene expression patterns appeared to be related to physiological properties of the cell lines, such as their doubling time in culture, drug metabolism or the interferon response. Comparison of gene expression patterns in the cell lines to those observed in normal breast tissue or in breast tumor specimens revealed features of the expression patterns in the tumors that had recognizable counterparts in specific cell lines, reflecting the tumor, stromal and inflammatory components of the tumor tissue. These results provided a novel molecular characterization of this important group of human cell lines and their relationships to tumors in vivo.
This study is described more fully in Ross DT et al.(2000) Nat Genet 24:227-35
Keywords: other

last: Ross

first: U

last: Scherf

last: Spellman

last: Waltham

middle: G

last: Myers

middle: N

last: Weinstein

last: Brown


title: P19 embryonic carcinoma (EC) cells induced to form cardiomyocytes in vitro

status: Public on Jul 18 2002

city: Baltimore

first: Kenneth

middle: R.

last: Boheler

address: 5600 Nathan Shock Drive

department: GRC

institute: National Institute on Aging, NIH

summary:
SAGE identification of differentiation responsive genes in P19 embryonic cells induced to form cardiomyocytes in vitro.
P19 embryonic carcinoma (EC) cells, induced to form cardiomyocytes in vitro - undifferentiated cells, day 3+0.5 and day 3+3.0 of differentiation protocol.
Keywords = EC cells, P19, differentiation, cardiomyocytes
Keywords: time-course

first: Sergey

middle: V

last: Anisimov

first: Kirill

last: Tarasov

first: Daniel

last: Riordon

first: Anna

last: Wobus


title: Ume6 regulon

status: Public on Jun 17 2002

city: Montpellier

first: Michel

last: Bellis

institute: CNRS

summary:
The Ume6 transcription factor in yeast is known to both repress and activate expression of diverse genes during mitotic growth and meiotic development. To obtain a more complete profile of the functions regulated by this protein, microarray analysis was used to examine transcription in wild type and ume6-deleted diploids during vegetative growth in glucose and acetate.
Keywords = yeast
Keywords = meiosis
Keywords = sporulation
Keywords = UME6
Keywords = micorarrays
Keywords = GeneChips
Keywords = bioinformatics
Keywords: other

first: R

last: Williams

last: Primig

first: B

last: Washburn

first: E

last: Winzeler

first: C

last: Sarrauste de MenthiSre

middle: W

last: Davis

last: Esposito

first: Roy

first: Michael

first: Brian

first: Elizabeth

first: Cyril

last: Sarrauste de Menthière

first: Ronald

first: Rochelle


title: Stresses induce gene expression in Arabidopsis

status: Public on Jun 19 2002

first: Zeji

last: Du

summary:
UV-B light and Gamma-ray treated plantlet.
Keywords: ordered

first: Angela

middle: D

last: Scott

first: Gregory

last: May