title: Common bile duct ligation time-course

summary:
Male Sprague-Dawley rats weighing 250-300 g were purchased from Japan SLC Co. (Shizuoka, Japan). The animals were housed under a daily controlled 12-h light and 12-h dark cycle at 23 °C with free access to rat chow (Japan SLC Co.) and water for 1 week prior to the experiments.
Rats were laparotomized under ether anesthesia in each experiment, and the common bile duct of each rat was ligated between the liver hilus and small intestine. Control animals underwent a sham operation with exposure but without ligation of the common bile duct. After the CBDL or sham operation, animals were allowed access to food and water ad libitum.
Groups of three rats were sacrificed under ether anesthesia at 1, 3 and 12 hr after the CBDL or sham operation. At the time of sacrifice, the right lateral liver lobe was removed and flash-frozen in liquid nitrogen and stored at -80 °C.
Total RNA isolated from frozen livers using TRIzol reagent (Invitrogen Co., Carlsbad, CA) was mixed to minimize variation among animals. Poly(A) RNA was purified using Oligotex-dT30 (Takara Shuzo Co., Ltd., Kyoto, Japan) in accordance with manufacturer’s instructions. Fluorescence-labeled probes were prepared by reverse transcription using a superscript II reverse transcriptase (Invitrogen Co.) and cyanine-3- and cyanine-5-dUTP (Perkin-Elmer Inc., Wellesley, MA). Poly(A) RNAs derived from rats that has undergone CBDL and from those that has undergone a sham operation were labeled with cyanine-3 and cyanine-5, respectively, and vise varsa. Fluorescence-labeled probes were purified using a MinElute PCR Products Purification Kit (Quiagen GmbH, Hilden, Germany) in accordance with manufacturer’s instructions. Each purified probe was suspended in hybridization buffer containing 1.6 mg/mL poly(A) (Roche Diagnostics, Basel, Switzerland) and yeast tRNA (Roche Diagnostics), 0.67 mg/mL herring sperm, 16% 20 x SSC and 0.3% SDS and applied to a cDNA microarray containing 1,800 rat genes on a slide glass (Asahi Technoglass Co., Tokyo, Japan). Three house-keeping genes (GAPDH, HPRT and b-actin) and rat unrelated traits (Lambda DNA) were also spotted on the slide as internal positive and negative controls, respectively.
Hybridization was carried out twice to eliminate any dye bias. In one experiment, duplicate slides were hybridized with probes derived from CBDL and control rats that had been labeld with cyanine-3 and cyanine-5, respectively. In a replicate experiment, other duplicate slides were hybridized with probes derived from CBDL rats and control rats that had been labeled with cyanine-5 and cyanine-3, respectively (color swap). Then, the slides were cover-slipped and incubated in a sealed chamber (Asahi Technoglass Co.) for 16 hrs under a humidified (65 °C) condition. After being washed in low-stringency buffer (2 x SSC and 0.1% SDS), high-stringency buffer (0.2 x SSC and 0.1% SDS) and 0.2 x SSC and then rinsing with 99.5% ethanol, the slide was dried by centrifugation at low speed and used for scanning.
Fluorescence was scanned by using a ScanArray 4000 (Packard BioChip Technologies, Billerica, MA) and quantified by using QuantArray Software (Packard BioChip Technologies, Billerica, MA).

Keywords: time-course


title: Longitudinal analysis of developing neointimal vascular proliferation and pulmonary hypertension in rats

status: Public on Dec 02 2003

city: Stanford

first: Peter

middle: N.

last: Kao

state: CA

address: 300 Pasteur Drive

department: Pulmonary and Critical Care Medicine

country: USA

institute: Stanford University Medical Center

summary:
6 timepoints: Day 0 (normal controls), progressively developing neointimal vascular proliferation and pulmonary hypertension in vehicle treated animals (Days 14, 21, 28 and 35) and triptolide-treated animals at Day 35.

Replicates:
6 for Day 0 (normal)
2 for Daty 14
3 each for Days 21, 28, 35 and Triptolide -treated at day 35 (T)

Keywords: time-course


title: time 24 hr to 0 hr

status: Public on Nov 25 2003

city: Adelaide

first: Anna

last: Tsykin

state: SA

address: Frome Road

department: Hanson Institute

country: Australia

institute: SA Pathology

summary:
Four dye swap replicates were performed with material derived 24 hours after stimulation of HUVECs with  PMA and RMAC11 hybridised to material obtained at time 0 hours.
The cDNAs used in this microarray were identified as part of collaborative project between the IMVS and Bionomics Limited. The project aims were to identify genes up-regulated during in vitro capillary tube formation as targets for angiogenesis-based therapeutics.

Any requests for further information regarding the data generated from this collaboration should be directed to Bionomics Limited (www.bionomics.com.au) at the
following address:

Bionomics Limited
31 Dalgleish Street
Thebarton, South Australia
Australia, 5031
Phone: 618 8354 6104
Fax: 618 8354 6199
Email: busdev@bionomics.com.au
Keywords = angiogenesis
Keywords = HUVEC
Keywords = in vitro
Keywords = capillary tube
Keywords: repeat sample

first: C

last: Hahn


title: time 6 hr to 0 hr

summary:
Four dye swap replicates were performed with material derived 6 hours after stimulation of HUVECs with  PMA and RMAC11 hybridised to material obtained at time 0 hours.
Keywords = angiogenesis
Keywords = HUVEC
Keywords = in vitro
Keywords = capillary tube
Keywords: repeat sample


title: time 0.5 hr to 0 hr

status: Public on Nov 26 2003

summary:
Six dye swap replicates were performed with material derived 0.5 hour after stimulation of HUVECs with  PMA and RMAC11 hybridised to material obtained at time 0 hours.
Keywords: repeat sample

first: J

middle: R

last: Gamble

first: M

middle: A

last: Vadas

middle: N

middle: J

last: Drogemuller

first: S

last: Waterman

first: A

first: G

last: Goodall


title: time 3 hr to 0 hr

summary:
Four dye swap replicates were performed with material derived 3 hour after stimulation of HUVECs with  PMA and RMAC11, hybridised to material obtained at time 0 hours.
Keywords: repeat sample


title: genes/pathways underlying lipoprotein homeostasis

status: Public on Nov 10 2003

city: Leiden

first: Nicole

last: Datson

department: Medical Pharmacology

country: Netherlands

institute: Leiden University

summary:
The aim of this study was to identify novel genes and pathways underlying lipoprotein homeostasis. The liver expression profile of mild hyperlipidemic E3L transgenic mice was compared to that of the wild-type B6 mice.
Keywords: parallel sample

first: Arja

last: Kreeft

first: Corina

last: Moen

first: Marten

last: Hofker

first: Rune

last: Frants

first: Erno

last: Vreugdenhil

first: Marion

last: Gijbels

first: Louis

last: Havekes


title: Corticosteroid responsive genes

status: Public on Oct 31 2003

summary:
Three groups of Wistar rats with different manipulated levels of corticosterone were used to identify corticosteroid-responsive genes in hippocampus:
1. rats were adrenalectomised (ADX)
2. In addition to ADX these rats were implanted with a subcutaneous pellet containing 20 mg corticosterone and 80% cholesterol (ADX + low CORT)
3. In addition to ADX and implantation of a corticosterone pellet, these rats received a subcutaneous injection with corticosterone (1 mg/kg bodyweight) three hours prior to decapitation ((ADX + low CORT) + acute high CORT).

All 3 groups of rats were decapitated three days after ADX and their hippocampus was isolated. Hippocampal RNA from 6 rats per group was pooled and used as input material for the SAGE libraries.
Keywords: parallel sample

first: Jeannette

last: van der Perk

first: E. Ronald

last: de Kloet


title: epileptogenesis

summary:
experimental group and control group in rat post-status epilepticus model.
Keywords: parallel sample

first: Erik

last: Hendriksen

first: Wim

last: Ghijsen

first: Erwin

last: van Vliet

first: Fernando

last: Lopes da Silva

first: Jan

last: Gorter


title: Porcine liver

status: Public on Nov 15 2003

city: Urbana

first: Yewon

last: Cheon

state: IL

institute: University of Illinois at Urbana Champaign

summary:
Fasting, fed, and Clofibric Acid comparisons
Keywords: other

first: Mark

last: Band

first: Jonathan

middle: E

last: Beever

first: Manabu

middle: T

last: Nakamura


title: short and long attack latency mice

first: Nicole

last: Datson

summary:
Two wild house mice lines were genetically selected for short and long attack latency. Mice with an attack latency <50s or >600s were considered short attack latency mice (SAL) and long attack latency mice(LAL) respectively. RNA from the hippocampus of 14 SAL or 14 LAL mice was pooled and used as input material for the SAGE libraries.
Keywords: other

first: Dorine

last: Feldker

first: Alexa

last: Veenema

last: Meulmeester


title: Expression of Annotated Genes

status: Public on Oct 30 2003

city: Albany

first: Atsunari

last: Tsuchisaka

address: 800 Buchanan St.

department: Plant Gene Expression Center

institute: University of California, Berkeley / USDA

type: Expression profiling by genome tiling array

summary:
Contains a row for each annotated gene in each sample, indicating whether our analysis called the gene "present" or "absent" in the sample. Gene names and coordinates refer to version 3 of the TIGR annotation as submitted to GenBank (GI numbers 22330780, 22326553, 22331929, 22329272, 22328163).
Keywords: other

first: Joseph

middle: M

last: Dale

first: Huaming

last: Chen

first: Rosa

last: Cheuk

first: Christopher

last: Kim

first: Jun

last: Lim

first: Curtis

last: Palm

first: Paul

last: Shinn

first: Audrey

last: Southwick

first: Hank

middle: C

last: Wu

first: Kayoko

last: Yamada

first: Ronald

middle: W

last: Davis

last: Ecker

first: Athanasios

last: Theologis


title: Expression in Intergenic Regions

summary:
Contains a row for each intergenic region in each sample, indicating whether our analysis called a window within the region "present" or "absent" in the sample. Intergenic regions are regions containing neither annotated genes nor intergenic clusters. Region coordinates refer to version 3 of the TIGR annotation as submitted to GenBank (GI numbers 22330780, 22326553, 22331929, 22329272, 22328163).
Keywords: other


title: Comparison of young and aged F344 rat coronary artery

status: Public on Oct 28 2003

city: Valhalla

first: Anna

last: Csiszar

state: NY

department: Physiology

institute: New York Medical College

summary:
Previous studies showed that aging in coronary arteries is associated with pro-inflammatory phenotypic changes and decreased NO bioavailability, which, we hypothesized, promotes vascular disease by inducing endothelial apoptosis. To test this hypothesis we characterized pro-apoptotic alterations in the phenotype of coronary arteries of aged (26 month old) and young (3 month old) F344 rats. DNA fragmentation analysis and TUNEL assay showed that in aged vessels there was a ~4 fold increase in the number of apoptotic endothelial cells. Analysis of the expression of apoptosis-related genes (real-time PCR) showed that in aged coronary arteries there was an increased expression of TNFa, TNFb, caspase 9 and an increased presence of cleaved caspase 3 and caspase 9 (Western blotting), whereas expression of TNFR1 and that of TRADD, Bcl-2, Bcl-X(L), Bid, Bax, caspase 8 and caspase 3 were unchanged. Vascular expression and activity of TNFa convertase enzyme were preserved in aging. We propose that aging-induced up-regulation of TNFa and decreased bioavailability of NO promote endothelial apoptosis in coronary arteries that may lead to the development of endothelial dysfunction and ischemic heart disease in the elderly.
Keywords: other


status: Public on Dec 12 2003

city: Daejon

first: Jin-Soo

country: South Korea

institute: ToolGen, Inc.

summary:
Toward a functional annotation of the human genome using artificial transcription factors.
Keywords: other


title: Abeta-activated Array Experiment

status: Public on Oct 29 2003

city: South San Francisco

first: Scott

middle: Curtis

last: Lohr

address: 290 Utah Ave.

department: Bioinformatics

institute: AGY Therapeutics Inc.

summary:
This series represents the samples used to generate the associated gene listing. The samples contained belong to two Platform accessions GPL561 and GPL562. There is a slight redundancy in the gene list due to multiple strong hits for a given gene. Clone selection was based on a fold >= 1.2 with a p-value <= 0.1 in at least 2 probe samples.
Keywords: other

first: L

last: Gan

first: S

last: Ye

first: A

last: Chu

first: K

last: Anton

last: Yi

first: V

last: Vincent

first: D

last: von Schack

last: Chin

first: J

last: Murray

last: Patthy

first: M

last: Gonzalez-Zulueta

last: Nikolich

first: R

last: Urfer


title: Young F344 rat coronary artery

summary:
Previous studies showed that aging in coronary arteries is associated with pro-inflammatory phenotypic changes and decreased NO bioavailability, which, we hypothesized, promotes vascular disease by inducing endothelial apoptosis. To test this hypothesis we characterized pro-apoptotic alterations in the phenotype of coronary arteries of aged (26 month old) and young (3 month old) F344 rats. DNA fragmentation analysis and TUNEL assay showed that in aged vessels there was a ~4 fold increase in the number of apoptotic endothelial cells. Analysis of the expression of apoptosis-related genes (real-time PCR) showed that in aged coronary arteries there was an increased expression of TNFa, TNFb, caspase 9 and an increased presence of cleaved caspase 3 and caspase 9 (Western blotting), whereas expression of TNFR1 and that of TRADD, Bcl-2, Bcl-X(L), Bid, Bax, caspase 8 and caspase 3 were unchanged. Vascular expression and activity of TNFa convertase enzyme were preserved in aging. We propose that aging-induced up-regulation of TNFa and decreased bioavailability of NO promote endothelial apoptosis in coronary arteries that may lead to the development of endothelial dysfunction and ischemic heart disease in the elderly.
Keywords: repeat sample


title: Aged F344 rat coronary artery

summary:
Previous studies showed that aging in coronary arteries is associated with pro-inflammatory phenotypic changes and decreased NO bioavailability, which, we hypothesized, promotes vascular disease by inducing endothelial apoptosis. To test this hypothesis we characterized pro-apoptotic alterations in the phenotype of coronary arteries of aged (26 month old) and young (3 month old) F344 rats. DNA fragmentation analysis and TUNEL assay showed that in aged vessels there was a ~4 fold increase in the number of apoptotic endothelial cells. Analysis of the expression of apoptosis-related genes (microarray, real-time PCR) showed that in aged coronary arteries there was an increased expression of TNFa, TNFb, caspase 9 and an increased presence of cleaved caspase 3 and caspase 9 (Western blotting), whereas expression of TNFR1 and that of TRADD, Bcl-2, Bcl-X(L), Bid, Bax, caspase 8 and caspase 3 were unchanged. We propose that aging-induced up-regulation of TNFa and decreased bioavailability of NO promote endothelial apoptosis in coronary arteries that may lead to the development of endothelial dysfunction and ischemic heart disease in the elderly.
Keywords: repeat sample

first: Zoltan

last: Ungvari


title: HEVEC dedifferentiation

status: Public on Oct 18 2003

city: Toulouse

first: Delphine-Armelle

last: Lacorre

address: 205, route de Narbonne

department: Protéome et Cibles Thérapeutiques

country: France

institute: IPBS - CNRS UMR 5089

summary:
A double screen has been carried out by comparing freshly isolated HEVEC (D0-Hevec) from human tonsils to freshly purified HUVEC (D0-Huvec), and to dedifferentiated HEVEC (D2-Hevec) grown ex vivo for two days, using three Clontech commercial nucleotide arrays (Atlas Human Cardiovascular, 1.2 I and 1.2II Arrays)
Keywords = freshly isolated HEVEC expression profile
Keywords = HEVEC dedifferentiation ex vivo
Keywords: other

first: Espen

middle: S

last: Baekkevold

first: Ignacio

last: Garrido

first: Per

last: Brandtzaeg

first: Guttorm

last: Haraldsen

first: François

last: Amalric

first: Jean-Philippe

last: Girard


title: 6 Auxins treatment

status: Public on Oct 12 2003

city: RTP,

first: Yang

last: Qiu

state: NC

address: 108 TW Alexander Dr.

department: Investigational Genomics

institute: Paradigm Genetics, Inc

summary:
Approximately 500 surface sterilized seeds of Arabidopsis seeds (ecotype: Col-0) were sterilely sown on filter disks overlaying solid ½ MS media 1% sucrose, stratified at 4C for 48 h and grown in darkness at 25C for 4 d. Seedlings were gently submerged by application to the plates of the different auxin solutions (made in ethanol carrier; 0.1% final concentration) and at the indicated times, the seedlings were lifted from the plate en mass and flash frozen in liquid nitrogen.
Keywords: repeat sample

first: John

last: Pufky

first: Rao

last: Mulpuri

first: Patrick

last: Hurban

first: Alan

last: Jones


status: Public on Oct 08 2003

city: La Jolla

first: Jih-tung

last: Pai

institute: The Burnham Institute

summary:
Comparison between EC and non-EC after EC purification in kidney and lung.
Keywords: other

first: Erkki

last: Ruoslahti


title: Chondrogenesis in ATDC5 cells

status: Public on Sep 10 2003

city: Neuherberg

first: Matthias

last: Wahl

address: Ingolstaedter Landstrasse 1

department: Institute of Developmental Genetics

country: Germany

institute: GSF - National Research Center for Environment and Health

summary:
SAGE analysis of early chondrogenesis in ATDC5 cells induced by BMP4
Keywords: time-course

middle: B

first: Chisa

last: Shukunami

first: Ulrich

last: Heinzmann

first: Kumiko

last: Hamajima

first: Yuji

last: Hiraki

first: Kenji

last: Imai


title: Iron chelation on human cytomegalovirus infected MRC-5 fibroblasts

status: Public on Sep 20 2003

city: Syracuse, New York

first: Lilia

last: Maglova-Crowe

address: 130 College Place, BRL

department: Biology

institute: Syracuse University

summary:
MRC-5 cells (American Type Culture Collection, Manassas, VA) derived from human lung fibroblasts (passages 19-25) were cultured in MEM with Earle’s salts, supplemented with 2 mM glutamine and 10% heat-inactivated FCS. Cells were grown in an incubator with a humidified atmosphere of 5% CO2 in air at 37oC for several days to reach confluence.
HCMV strain AD169 (American Type Culture Collection, Manassas, VA) was used in these studies. A continually replenished stock of HCMV was cultured in confluent MRC-5 cells. At the appropriate time, the infected cells were lysed and the infectivity of the resultant viral stock was assayed by plaque assay. For the studies reported here, HCMV infection was carried out by exposing the confluent MRC-5 cells to a virus stock at a multiplicity of infection (MOI) of ~3-5 plaque-forming units (PFU) per cell for 1 h at 370C. To control for non-specific effects of the cell lysate portion of the viral stock, a parallel set of MRC-5 cells were always mock infected by a 1h exposure to a lysate of uninfected MRC-5 cells. After the infectious period of exposure, both mock- and virus-treated cells were rinsed with phosphate buffered saline (PBS) followed by fresh culture medium and returned to cell culture for various post-exposure (PE) times.
Mock- or HCMV-infected cells were homogenized in guanidinium isothiocyanate, followed by the isolation of total RNA following the method of Chirgwin et al. (PubMed ID 518835). Purity and integrity of the RNA were checked spectroscopically and by gel electrophoresis prior to use. Two successive oligo (dT) cellulose columns were then used to isolate poly A+ RNA for microarray analysis, yielding 600 ng of mRNA per channel (mock-infected or HCMV-infected cells). These were labeled with Cy3 and Cy5 dyes respectively prior to hybridization with a UniGEM V cDNA microarray (Incyte Genomics, St Louis, MO).
Keywords: other

first: W

last: Crowe

first: L

last: Maglova

first: P

last: Ponka

first: J

last: Russell


title: Bladder cancer cells

status: Public on Nov 03 2003

city: Oklahoma City

first: Robert

middle: Evan

last: Hurst

state: OK

address: 920 S. L. Young Blvd

department: Urology

institute: Oklahoma University Health Sciences Center

summary:
Examination of gene expression in several bladder cancer cell lines grown on either plastic, SIS (small intestine submucosa) gel or matrigel.
A data table of normalized values is appended below.  Data were normalized as described in detail by Knowlton N, Dozmorov IM, Centola M. Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics. 2004 Dec 12;20(18):3687-90.
In brief, the normalization method relies on a number of low expression genes to provide an estimate of non-specific binding.  This information is then used to perform a Z transformation on the data.  Once normalized the data are "unbiased" through robust linear regression to allow comparisons across different membranes.
Keywords: other

first: Igor

last: Dozmorov

first: Kimberly

middle: D

last: Kyker

first: Craig

last: Cadwell

first: Michael

last: Centola


title: Control and Congestive Heart Failure

status: Public on Sep 08 2003

city: Tucson

first: Niranjan

last: Maitra

state: AZ

address: 1501 North Campbell Avenue

department: Sarver Heart Center

institute: University of Arizona

summary:
Congestive heart failure was done by artificial myocardial infarction. After extracting total RNA from control and infarcted ventricles with Triazol, messenger RNA was isolated with Qiagen mRNA isolation kit. About 1.5ug poly A+ RNA was taken for probe preparation. Probe was labeled with Alexa Fluor 546 and 657. Labeled probes were hybridized with Qiagen rat unigene oligo library. After 2 low and 1 high stringency washes Prolong Antifade was added to the slides to prevent bleaching effect. The data ratio was normalized using a location and intensity dependent Lowess formula.
Keywords: other


title: Kidney EC and non-EC comparison array B

first: Jih-tung

last: Pai

summary:
Four sets of kidney EC and non-EC comparisons and the calculated mean.
Keywords: repeat sample

first: Erkki

last: Ruoslahti


title: indole-3-acetic acid (IAA) time course

first: Yang

last: Qiu

summary:
Approximately 500 surface sterilized seeds of Arabidopsis seeds (ecotype: Col-0) were sterilely sown on filter disks overlaying solid ½ MS media 1% sucrose, stratified at 4C for 48 h and grown in darkness at 25C for 4 d. Seedlings were gently submerged by application to the plates of the different auxin solutions (made in ethanol carrier; 0.1% final concentration) and at the indicated times (20 min, 40 min, 60 min), the seedlings were lifted from the plate en mass and flash frozen in liquid nitrogen.
Keywords: time-course

first: John

last: Pufky

first: Rao

last: Mulpuri

first: Patrick

last: Hurban

first: Alan

last: Jones


title: Rapid molecular responses of maize to UV-B: gene expression profiling in irradiated and shielded tissues

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 UV-B responses in both directly exposed and shielded tissues of a maize line deficient in anthocyanin accumulation.  Among 347 transcripts found to be regulated after 8 h of high UV-B irradiation, 285 were increased significantly in at least one organ but only 80 were down-regulated by UV-B.  Although some genes were regulated by UV-B in more than one sample, most UV-B regulated genes were organ-specific.  A larger number of transcript changes occurred in directly exposed than in shielded organs, and more transcripts levels were changed in adult than in seedling tissues.  Because shielded tissues including roots, immature ears, and leaves covered with a plastic that absorbs UV-B exhibited altered transcriptome profiles after plant exposure to UV-B, some signal(s) must be transmitted from irradiated to shielded tissues. The time course of transcript abundance changes monitored by RNA blot hybridization and real time RT-PCR indicated that the response kinetics to UV-B are very rapid as some transcript levels are altered within 1 h exposure, in both exposed and shielded tissues.   As the same total UV-B irradiation dose applied at three intensities elicited different transcript profiles, transcriptome changes do not show reciprocity.  Confirming and extending prior microarray hybridization results, supplemental UV-B increased expression of stress response and ribosomal protein genes, while photosynthesis-associated genes were down regulated in adult leaves.
Keywords: other

first: Virginia

last: Walbot


title: Lung EC and non-EC comparison array A

summary:
Four sets of lung EC and non-EC comparisons and the calculated mean.
Keywords: repeat sample


title: Lung EC and non-EC comparison array B

summary:
Six sets of kidney EC and non-EC comparisons and the calculated mean.
Keywords: repeat sample


title: Antisense Expression of Annotated Genes

first: Atsunari

last: Tsuchisaka

summary:
Contains a row for each annotated gene in each sample, indicating whether our analysis called the region antisense to the coding region of the gene "present" or "absent" in the sample. Gene names and coordinates refer to version 3 of the TIGR annotation as submitted to GenBank (GI numbers 22330780, 22326553, 22331929, 22329272, 22328163).
Keywords: other

first: Joseph

last: Dale

first: Huaming

last: Chen

first: Rosa

last: Cheuk

first: Christopher

last: Kim

first: Jun

last: Lim

first: Curtis

last: Palm

first: Paul

last: Shinn

first: Audrey

last: Southwick

first: Hank

last: Wu

first: Kayoko

last: Yamada

first: Ronald

last: Davis

last: Ecker

first: Athanasios

last: Theologis


title: Native versus cultured retinal pigment epithelium cells

status: Public on Oct 15 2003

city: Baltimore

first: James

last: Handa

state: MD

address: 600 N. Wolfe St.

department: Wilmer Eye Institute

institute: Johns Hopkins Medical Institutes

summary:
I. Exp Design
1. Type of experiment: Comparison of native versus cultured RPE cells
2. Experimental factors: Native RPE versus ARPE-19 cells grown on different matrices
3. How many hybridizations in exp: 21
4. If a common reference used for all the hybs: no
5. Quality control steps: three independent arrays for each condition
6. Description: The expression profile of ARPE-19 cells grown on different matrices were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 3 donors.

II. Samples used, extract prep, and labeling
1. Biosource: Human donor globes from NDRI (63, 71, 74 years old) and ARPE-19 cells.
2. Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (plastic, Matrigel, collagen I, collagen IV, laminin, and fibronectin).
3. Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer’s instructions.
4. Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP.
5. No external controls were added.

III. Hybridization procedures and parameters
1. Sample, array type, batch and serial # used
2. Hybridization protocol: Hybridization was carried out using the manufacturer’s recommendations. Arrays were prehybridized with Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS.
IV. Measurement data and specifications of data processing
1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis.
3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.
Keywords: other

first: J


title: Interstitial cystitis and antiproliferative factor treatment

status: Public on Sep 03 2003

first: Susan

last: Keay

institute: University of Maryland, Baltimore

summary:
Changes in human bladder epithelial cell gene expression associated with interstitial cystitis or antiproliferative factor treatment.

Explanted bladder epithelial cells from patients with interstitial cystitis (IC) have been shown to differ from explanted control cells in several ways, including production of an antiproliferative factor (APF), altered production of certain epithelial growth factors, and rate of proliferation. To better understand the role of the APF in abnormal bladder epithelial cell proliferation in IC, we studied gene expression patterns in normal bladder epithelial cells treated with APF vs. mock APF and compared them to expression patterns in IC vs. normal cells using microarray analysis. Oligo-dT-primed total cellular RNA was labeled with [33P]dCTP and hybridized to GeneFilter GF211 microarray membranes (Research Genetics) containing cDNA for 3,964 human genes. Thirteen genes that function in epithelial cell proliferation or differentiation were consistently differentially expressed in both IC (compared with control) and APF-treated (compared with mock APF-treated) normal bladder epithelial cells. The general pattern of gene expression in IC and APF-treated cells suggested a less proliferative phenotype, with increased expression of E-cadherin, phosphoribosylpyrophosphate synthetase-associated protein 39, and SWI/SNF complex 170-kDa subunit, and decreased expression of vimentin, {alpha}2-integrin, {alpha}1-catenin, cyclin D1, and jun N-terminal kinase 1; these findings were confirmed for the structural gene products (E-cadherin, vimentin, {alpha}2-integrin, and {alpha}-catenin) by immunohistochemistry. These results are compatible with the previously noted decreased proliferation rate of IC and APF-treated normal cells, and indicate that the mechanism whereby APF inhibits cell proliferation may involve both downregulation of genes that stimulate cell proliferation along with upregulation of genes that inhibit cell growth.
Keywords: other

first: S

first: F

last: Seillier-Moiseiwitsch

first: C

last: Zhang

first: T

last: Chai


title: BMM_C3H/HeJ_LPS_timecourse

status: Public on Mar 28 2003

city: San Diego

first: Timothy

last: Ravasi

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California-San Diego

summary:
Bone marrow derived macrophages (BMM) total RNA from C3H/ARC mice extracted after stimulation by LPS at different time points.
Each time point stimulated with 10ug/ml LPS from Salmonella minnesota for the time indicated.
The RNA from each BMM stimulated time point was labeled with Cy3 and compared with a common reference (total RNA from C57BL6/J 17.5 embryo) labeled with Cy5.
Keywords = LPS, macrophages, innate immunity
Keywords: time-course

first: Christine

last: Wells

first: Razvan

last: Sultana

first: Ken

last: Yagi

first: Piero

last: Carninci

first: Hidemasa

last: Bono

first: Geoffrey

last: Faulkner

first: Yasushi

last: Okazaki

first: John

last: Quackenbush

first: David

last: Hume

last: Lyons


title: Gene expression profiles in normal and Otx2-/- early gastrulating mouse embryos

status: Public on Sep 25 2003

city: 91191 Gif/ Yvette Cedex

first: Jean-Marc

last: Elalouf

department: IBITEC-S

institute: CEA Saclay

summary:
We compared gene expression profiles in wild-type and Otx2(-/-) 6.5 days postcoitum embryos by using a serial analysis of gene expression assay adapted to microdissected structures. Among a broader list, the study of six genes found to be differentially expressed allows defining a role for Otx2 in the orchestration of cell movements leading to the adequate organization of the embryo before gastrulation.
Keywords: other

first: Lise

last: Zakin

first: Bruno

last: Reversade

first: Berangere

last: Virlon

first: Christophe

last: Rusniok

first: Philippe

last: Glaser

last: Brulet


title: Kidney EC and non-EC comparison array A

first: Jih-tung

last: Pai

first: Erkki

last: Ruoslahti


title: UMRR vs Liver

status: Public on Mar 07 2003

city: Pasadena

first: Sangdun

last: Choi

address: 1200 E. California Blvd

institute: California Institute of Technology

summary:
UMRR (Universal Mouse Reference RNA, Catalog #740100) was purchased from Stratagene and used as the starting material. Liver total RNA (Catalog #64042-1) was purchased from Clontech and used as the starting material. UMRR 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

last: Cao

first: Sun-Young

last: Lee

first: Jong-Woo

last: Kim

first: Mi Sook

last: Chang

first: Melvin

middle: I

last: Simon


title: UMRR vs Spleen

summary:
UMRR (Universal Mouse Reference RNA, Catalog #740100) was purchased from Stratagene and used as the starting material. Spleen total RNA (Catalog #64044-1) was purchased from Clontech and used as the starting material. UMRR was labeled with Cyanine-3 (Green) while spleen was labeled with Cyanine-5 (Red). cRNA was made by the single round amplification method.
Keywords: repeat sample


title: Spleen vs Liver - cDNA - Double

status: Public on Mar 06 2003

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 double round amplification method.
Keywords: repeat sample


title: BMM_BalbC_LPS_timecourse

first: Timothy

last: Ravasi

first: Christine

last: Wells

first: Razvan

last: Sultana

first: Ken

last: Yagi

first: Piero

last: Carninci

first: Hidemasa

last: Bono

first: Geoffrey

last: Faulkner

first: Yasushi

last: Okazaki

last: Quackenbush

last: Hume

first: Paul


title: BMM_C3H/ARC_LPS_timecourse

first: John

first: David

last: Lyons


title: Spleen vs Liver - cDNA - Single

first: Sangdun

last: Choi

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


title: NGS_mouse_liver

status: Public on Nov 04 2002

city: Madison

first: Todd

last: Richmond

state: WI

address: One Science Court

institute: NimbleGen Systems Inc.

summary:
Replicate hydridizations with mouse liver mRNA.
Keywords: repeat sample

first: E

middle: F

last: Nuwaysir

first: W

last: Huang

first: T

last: Albert

first: J

last: Singh

first: K

first: A

last: Pitas

last: Gorski

middle: P

last: Berg

last: Ballin

first: M

last: McCormick

last: Norton

last: Pollock

last: Sumwalt

first: L

last: Butcher

first: D

last: Porter

last: Molla

first: C

last: Hall

first: F

last: Blattner

last: Sussman

first: R

middle: L

last: Wallace

last: Cerrina

last: Green


title: NGS_mouse_spleen

last: Richmond

summary:
Replicate hybridizations using mouse spleen mRNA
Keywords: repeat sample

last: Nuwaysir

last: Huang

last: Albert

last: Singh

last: Pitas

middle: R


title: Transcriptome of a mouse kidney cortical collecting duct cell line: effects of aldosterone and vasopressin

status: Public on Sep 24 2003

first: Jean-Marc

last: Elalouf

summary:
In this study, we analyzed the transcriptome of a highly differentiated mouse clonal CCD principal cell line (mpkCCD(cl4)) and the changes in the transcriptome induced by aldosterone and vasopressin. Serial analysis of gene expression (SAGE) was performed on untreated cells and on cells treated with either aldosterone or vasopressin for 4 h. The transcriptomes in these three experimental conditions were determined by sequencing 169,721 transcript tags from the corresponding SAGE libraries. Limiting the analysis to tags that occurred twice or more in the data set, 14,654 different transcripts were identified, 3,642 of which do not match known mouse sequences. Statistical comparison (at P < 0.05 level) of the three SAGE libraries revealed 34 AITs (aldosterone-induced transcripts), 29 ARTs (aldosterone-repressed transcripts), 48 VITs (vasopressin-induced transcripts) and 11 VRTs (vasopressin-repressed transcripts). A selection of the differentially-expressed, hormone-specific transcripts (5 VITs, 2 AITs and 1 ART) has been validated in the mpkCCD(cl4) cell line either by Northern blot hybridization or reverse transcription-PCR. The hepatocyte nuclear transcription factor HNF-3-alpha (VIT39), the receptor activity modifying protein RAMP3 (VIT48), and the glucocorticoid-induced leucine zipper protein (GILZ) (AIT28) are candidate proteins playing a role in physiological responses of this cell line to vasopressin and aldosterone.
Keywords: other

first: Maya

last: Robert-Nicoud

first: Marjorie

last: Flahaut

first: Marie

last: Nicod

first: Miguel

last: Salinas

first: Marcelle

last: Bens

first: Alain

last: Doucet

first: Patrick

last: Wincker

first: François

last: Artiguenave

first: Jean-Daniel

last: Horisberger

last: Vandewalle

first: Bernard

last: Rossier

first: Dmitri

last: Firsov


title: Cold stress in sugarcane exp2

status: Public on Jan 03 2003

city: Campinas

first: Fábio

middle: Tebaldi

last: Nogueira

department: CBMEG

country: Brazil

institute: Institute of Biology

summary:
Tropical and subtropical plants are generally sensitive to cold and can show appreciable variation in their response to cold stress when exposed to low positive temperatures. Using nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp.) exposed to cold for 3-48 h. Thirty-four cold-induced ESTs were identified, of which 23 were novel cold-responsive genes that had not previously been reported as being cold-inducible. This series has the samples from replicate experiment number 2.
Keywords = sugarcane
Keywords = cold
Keywords = nylon arrays
Keywords: time-course

first: Fabio

first: Vicente

last: De Rosa Jr

first: Marcelo

last: Menossi

first: Eugenio

last: Ulian

first: Paulo

last: Arruda


title: Cold stress in sugarcane exp1

summary:
Tropical and subtropical plants are generally sensitive to cold and can show appreciable variation in their response to cold stress when exposed to low positive temperatures. Using nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp.) exposed to cold for 3-48 h. Thirty-four cold-induced ESTs were identified, of which 23 were novel cold-responsive genes that had not previously been reported as being cold-inducible. This series has the samples from replicate experiment number 1.
Keywords = sugarcane, cold, nylon arrays
Keywords: time-course


title: Expression of Intergenic Clusters

status: Public on Oct 30 2003

city: Albany

first: Atsunari

last: Tsuchisaka

institute: University of California, Berkeley / USDA

summary:
Contains a row for each intergenic cluster in each sample, indicating whether our analysis called the cluster "present" or "absent" in the sample. Intergenic clusters are novel (unannotated) genes detected by aligning Arabidopsis cDNAs/ESTs to the genome. Cluster coordinates refer to version 3 of the TIGR annotation as submitted to GenBank (GI numbers 22330780, 22326553, 22331929, 22329272, 22328163).
Keywords: other

first: Joseph

last: Dale

first: Huaming

last: Chen

first: Rosa

last: Cheuk

first: Christopher

last: Kim

first: Jun

last: Lim

first: Curtis

middle: J

last: Palm

first: Paul

last: Shinn

first: Audrey

last: Southwick

first: Hank

last: Wu

first: Kayoko

last: Yamada

first: Ronald

last: Davis

last: Ecker

first: Athanasios

last: Theologis