title: Temporal bovine liver gene expression

status: Public on Aug 10 2005

city: Urbana

first: Juan

middle: J.

last: Loor

state: IL

address: 1207 West Gregory Drive

department: Animal Sciences

institute: University of Illinois

summary:
Liver from five Holstein cows fed to current National Research Council (2001) recommendations during the dry period and early lactation was biopsied at -65, -30, -14, 1, 14, 28, and 49 days relative to parturition.  cDNA from liver and a reference standard (made from cattle tissues not including liver or mammary) were labeled with Cy3 or Cy5 fluorescent dye and co-hybridized to our 7,872 bovine cDNA microarray using a dye-swap design. More than 5,000 sequences present on the array were expressed in liver.  Normalized log-transformed ratios (liver/reference) were analyzed using a MIXED model in SAS.  Keywords: cow, liver, lactation, microarray, periparturient period
Keywords: time-course

middle: J

first: Heather

middle: M

last: Dann

first: Robin

last: Everts

first: Rosane

last: Oliveira

first: Cheryl

last: Green

first: Nicole

last: Janovick Guretzky

first: Sandra

middle: L

last: Rodriguez-Zas

first: Harris

last: Lewin

first: James

middle: K

last: Drackley


title: Gene expression profiling of pancreatic cancer cell conditioned myoblasts.

status: Public on Oct 05 2005

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary:
We verified whether conditioned media (CM) from pancreatic cancer cell lines (MIAPaCa2, CAPAN-1, PANC-1, BxPC3) alter glucose metabolism and gene expression profiles (microarray experiment with a platform of 5000 skeletal muscle cDNA) in mice myoblasts.
Myoblasts were incubated with control or pancreatic cancer CM for 14 and 24 hours.
Lactate significantly increased in CM compared with non-conditioned myoblasts. No variations in expression levels of the main genes involved in glycolysis were found in CM myoblasts. Propionyl coenzyme A carboxylase and isocitrate dehydrogenase 3 beta genes, which encode enzymes of the tricarboxylic acid cycle, were overexpressed, while IGFIIR and VAMP5 genes were underexpressed in CM myoblasts. PAFAH1B1 and BCL-2 genes (intracellular signal transduction) and the serine protease cathepsin G (proteolysis), were overexpressed in CM myoblasts. Tyrosine accumulation in CM myoblasts suggested that proteolysis overcomes protein synthesis. Sorcin, actin alpha, troponin T1, and filamin A were underexpressed in CM myoblasts.
Our findings demonstrate that pancreatic cancer cell conditioned media enhanced lactate production and induced proteolysis, possibly by altering expression levels of a large number of genes, not only those involved in protein biosynthesis and degradation or glucose metabolism, but also those involved in the tricarboxylic acid cycle and in vesicle traffic.
Keywords: Mice myoblasts, pancreatic cancer cell lines (MIAPaCa2, CAPAN-1, PANC-1, BxPC3), cDNA microarrays

overall_design:
Myoblasts were incubated with control (MBN) or CAPAN-1 pancreatic cancer conditioned media (MBC) for 0, 14 and 24 hours.
RNAs purified from MBC at 14 and 24 hours were compared with RNA from MBN at 0 hour and at the corresponding stages.
These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 2.0). Two replicates of each experiment were performed using different microarray slides, in which sample and reference RNAs, labeled either with Cy3 or Cy5 fluorochromes, were crossed in both combinations (dye-swapping procedure).

first: Daniela

last: Basso

first: Caterina

last: Millino

first: Eliana

last: Greco

first: Chiara

last: Romualdi

first: Paola

last: Fogar

first: A

last: Valerio

first: Milena

last: Bellin

first: Carlo

last: Zambon

first: F

last: Navaglia

first: N

last: Dussini

first: Andrea

last: Avogaro

first: S

last: Pedrazzoli

first: Mario

last: Plebani


title: Heart Transplant Rejection Profiling in Peripheral Blood

status: Public on Sep 01 2005

city: South San Francisco

first: Expression

last: Diagnostics

state: CA

address: 750 Gateway Boulevard, Suite H

country: USA

institute: XDx Inc

summary:
PBMC samples from heart transplant patients were profiled. Sample classification was based on endomyocardial biopsy at the time of sample collection.
Keywords = Transplant
Keywords = Transplantation
Keywords = Heart Transplant
Keywords = Graft Rejection
Keywords = Rejection
Keywords = PBMC
Keywords = Immune Response
Keywords = Peripheral Blood
Keywords: other

middle: C

last: Deng

first: Howard

last: Eisen

first: Mandeep

middle: R

last: Mehra

first: Margaret

last: Billingham

first: Charles

last: Marboe

first: Gerald

last: Berry

first: Jon

last: Kobashigawa

first: Frances

last: Johnson

first: Randall

last: Starling

first: Srinivas

last: Murali

first: Daniel

middle: F

last: Pauly

first: Sharon

last: Hunt

first: Jay

last: Wohlgemuth

first: Steve

last: Rosenberg

first: Preeti

last: Lal

first: Helen

last: Baron

first: Tod

last: Klingler

first: Dirk

last: Walther

first: Robert

last: Woodward


title: Six1 and Six4 target genes in mk4 cells

status: Public on Jul 20 2005

city: Minamikawachi

first: Shigeru

last: Sato

state: Tochigi

address: Yakushiji

department: Division of Biology

country: Japan

institute: Jichi Medical School

summary:
To identify Six1 target genes, we chose the mK4 cell line that represents later metanephric mesenchyme of the embryonic kidney. The cells were infected with adenovirus vectors (AxCAwt) overexpressing VP16-Six1wt or VP16-Six1W171R and cultured for 24h. Total RNA was extracted using Isogen reagent (Nippon Gene), treated with RNase-free DNase (Roche Diagnostics) and purified with RNeasy Midi Kit (QIAGEN). Poly A+ RNA was selected using Oligotex-dT30  latex beads (TaKaRa). Poly A+ RNA (20 µg) was reverse transcribed using an oligo(dT) primer in the presence of aminoallyl dUTP without the addition of spike-in controls. Then, single-stranded cDNAs were coupled with Cy3 (AxCAwt VP16-Six1wt infected sample) or Cy5 (AxCAwt VP16-Six1W171R infected sample) dyes, and the labeled probes were purified with QIAquick PCR Purification kit (QIAGEN). Hybridization to the microarray was carried out at 65°C for 17h according to the manufacturer's instruction. The arrays were washed, dried and scanned using ScanArray 5000 (GSI Lumonics) at two different PMT voltage settings (high and low) to avoid signal saturation. Cy3 and Cy5 intensities for each spot on the array were determined by QuantArray software (Version 3.0.0.0, GSI Lumonics). The raw data thus obtained was processed and the Cy3 to Cy5 ratios were calculated as follows: 1) subtraction of the fluorescence intensity of negative control spots as background from the intensity of each of the Cy3 and Cy5 spots, 2) normalization of the entire data set using the global normalization method, 3) elimination of spots with high background intensity for either dye, and 4) determination of the Cy3 to Cy5 ratios.

To identify Six4 target genes, we chose the mK4 cell line that represents later metanephric mesenchyme of the embryonic kidney. The cells were infected with adenovirus vectors (AxCAwt) overexpressing VP16-Six4wt or VP16-Six4W263R and cultured for 24h. Total RNA was extracted using Isogen reagent (Nippon Gene), treated with RNase-free DNase (Roche Diagnostics) and purified with RNeasy Midi Kit (QIAGEN). Poly A+ RNA was selected using Oligotex-dT30  latex beads (TaKaRa). Poly A+ RNA (20 µg) was reverse transcribed using an oligo(dT) primer in the presence of aminoallyl dUTP without the addition of spike-in controls. Then, single-stranded cDNAs were coupled with Cy3 (AxCAwt VP16-Six4wt infected sample) or Cy5 (AxCAwt VP16-Six4W263R infected sample) dyes, and the labeled probes were purified with QIAquick PCR Purification kit (QIAGEN). Hybridization to the microarray was carried out at 65°C for 17h according to the manufacturer's instruction. The arrays were washed, dried and scanned using ScanArray 5000 (GSI Lumonics) at two different PMT voltage settings (high and low) to avoid signal saturation. Cy3 and Cy5 intensities for each spot on the array were determined by QuantArray software (Version 3.0.0.0, GSI Lumonics). The raw data thus obtained was processed and the Cy3 to Cy5 ratios were calculated as follows: 1) subtraction of the fluorescence intensity of negative control spots as background from the intensity of each of the Cy3 and Cy5 spots, 2) normalization of the entire data set using the global normalization method, 3) elimination of spots with high background intensity for either dye, and 4) determination of the Cy3 to Cy5 ratios.
Keywords: other

first: Zen-ichi

last: Ando

first: Keiko

last: Ikeda

first: Kiyoshi

last: Kawakami


title: Response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source.

status: Public on Aug 25 2005

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
The global gene expression program that accompanies the adaptation of Saccharomyces cerevisiae to an abrupt transfer from a fermentable to a nonfermentable carbon source was characterized by using a cDNA microarray to monitor the relative abundances and polysomal distributions of mRNAs. Features of the program included a transient reduction in global translational activity and a severe decrease in polysome size of transcripts encoding ribosomal proteins.
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
Keywords: replicate_design

overall_design: Using regression correlation

first: Peter

last: Sarnow


title: Intrinsic histone-DNA interactions and low nucleosome density are important for accessibility of promoters in yeast

status: Public on Jun 15 2005

city: Boston

first: Kevin

last: Struhl

state: MA

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

type: Genome binding/occupancy profiling by array

type: Genome binding/occupancy profiling by genome tiling array

summary:
In yeast cells, preferential accessibility of the HIS3-PET56 promoter region is determined by a general property of the DNA sequence, not by defined sequence elements.  In vivo, this region is largely devoid of nucleosomes, and accessibility is directly related to reduced histone density.  The HIS3-PET56 and DED1 promoter regions associate poorly with histones in vitro, indicating that intrinsic nucleosome positioning and stability is a major determinant of preferential accessibility.  Specific and genome-wide analyses indicate that low nucleosome density is a very common feature of yeast promoter regions that correlates poorly with transcriptional activation.  Thus, the yeast genome is organized into structurally distinct promoter and non-promoter regions, whose DNA sequences inherently differ with respect to nucleosome formation.  This organization ensures that transcription factors bind preferentially to appropriate sites in promoters, rather than to the excess of irrelevant sites in non-promoter regions.
Keywords: other

first: Edward

middle: A

last: Sekinger

first: Zarmik

last: Moqtaderi


title: Epigenetic treatment of cervical carcinoma cell lines

status: Public on Jul 17 2005

city: Seattle

first: Pavel

last: Sova

state: WA

address: 325 9th Avenue

department: Department of Pathology

institute: University of Washington

summary:
Four cervical carcinoma cell lines (C4I, CaSki, HeLa, SiHa) were treated with epigenetic modifying drugs 5-aza-2’-deoxycytidine and trichostatin A.  Such treatment leads to reactivation of genes that are epigenetically silenced in cancer by aberrant methylation; reactivated genes were then identified by microarray profiling.  Subsets consist of 2 biological repeats and 2 dye-flip experiments for each repeat for CaSki cell line, and 3 repeats, each with 2 dye-flip experiments for C4I, HeLa, Caski cell lines.  The identification of reactivated genes, their selection for validation experiments, and final identification of 6 genes that are significantly more often hypermethylated in cervical carcinoma clinical specimens is described in (manuscript submitted).
Keywords: other

first: Qinghua

last: Feng

first: Gary

last: Geiss

first: Troy

last: Wood

last: Strauss

first: Vania

last: Rudolf

first: Andre

last: Lieber

first: Nancy

middle: B

last: Kiviat

first: N


title: Agilent striptease

status: Public on Aug 20 2005

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary:
new and stripped microarrays
Keywords: reuse of Agilent custom 8.4 in situ microarrays

overall_design: Experimental design of two-color microarrays and naming scheme for validation of the stripping protocol. Individual experiments are designated [A(n)H(m)exp(o)] with microarrays being specified as [A(n)], hybridizations being specified as [H(m)] and experiments being specified as [exp(o)] where 1 =< n,m,o >= 4.


title: with and without EBV infection in NPC cell lines

status: Public on Jun 07 2005

city: Taipei

first: Yuan-Chii

middle: Gladys

last: Lee

department: Graduate Institute of Medical Informatics

country: Taiwan

institute: Taipei Medical University

summary:
5 samples with EBV infection vs 5 samples without
Keywords: parallel sample

middle: G

first: Chi-Ying

last: Huang

first: Chin-Tarng

last: Lin


title: Nasopharyngeal carcinoma (NPC) cell lines

summary:
5 EBV-free nasopharyngeal carcinoma cell lines expression patterns again normal epithelial tissues.
Keywords: repeat sample


title: Analysis of Gastric Cancer

status: Public on Jul 25 2005

city: SG

first: Amit

last: Aggarwal

department: Cellular and Molecular Research

country: Singapore

institute: National Cancer Centre of Singapore

summary:
To be completed by submitter
Keywords: other


title: Expression profiling of desmoid tumors and nodular fasciitis

city: Epalinges

first: Eugenia

last: Migliavacca

state: Vaud

address: Ch des Boveresses 155

country: Switzerland

institute: ISREC

summary:
Nodular fasciitis (NF) is a rapidly growing cellular mass composed of fibroblasts/myofibroblasts, usually localized in subcutaneous tissues, that typically undergoes fibrosis and almost never recurs. Desmoid tumors (DT) are rare forms of fibroblastic/myofibroblastic growth that arise in deep soft tissues, display propensity for local infiltration and recurrence but fail to metastasize. Given that both entities are primarily fibroblastic/myofibroblastic lesions with overlapping histological features, we compared their gene expression profile to identify differentially expressed genes that may provide not only potential diagnostic markers but also clues as to the pathogenesis of each disorder. Differentially expressed transcripts (89 clones displaying increased expression in DT and 246 clones displaying increased expression in NF), included genes encoding several receptor and non-receptor tyrosine kinases (EPHB3, PTPRF, GNAZ, SYK, LYN, EPHA4, BIRC3), transcription factors (TWIST1, PITX2, EYA2, OAS1, MITF, TCF20), and members of the Wnt signaling pathway (AXIN2, WISP1, SFRP). Remarkably, almost one fourth of the differentially expressed genes encode proteins associated with inflammation and tissue remodeling, including members of the interferon (IFN), tumor necrosis factor (TNF) and transforming growth factor beta (TGF-beta) signaling pathways as well as metalloproteinases (MMP1, 9, 13, 23), urokinase plasminogen activator (PLAU) and cathepsins. Our observations provide the first comparative molecular characterization of desmoid tumors and nodular fasciitis and suggest that selected tyrosine kinases, transcription factors and members of the Wnt, TGF-beta, IFN and TNF signaling pathways may be implicated in influencing and distinguishing their fate.
Keywords: comparative genomic hybridization

overall_design:
12 desmoid tumors and 6 nodular fasciitis were analyzed using MRC5 as common reference.
One duplicate with dye swap was performed (DT1 dye-swap)

first: Marina

last: Bacac

first: Thomas

last: Mckee

first: Mauro

last: Delorenzi

first: Jean-Michel

last: Coindre

first: Luis

last: Guillou

first: Ivan

last: Stamenkovic


title: p53 In Inflamatory Stress Response

status: Public on Dec 01 2005

city: Bethesda

first: Ana

middle: I

last: Robles

state: MD

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

summary:
Activation of the p53 network plays a central role in the inflammatory stress response associated with ulcerative colitis, and may modulate cancer risk in patients afflicted with this chronic disease. The overall goal of these experiments is to study the gene expression profiles associated with four microenvironmental components of the inflammatory response (NO*, DNA damage, DNA replication arrest, and hypoxia) that result in p53 stabilization and activation. To this end, isogenic HCT116 and HCT116 TP53-/- colon cancer cells were exposed to the NO*-donor Sper/NO, H2O2 (DNA damage), hypoxia, or hydroxyurea (HU, DNA replication arrest), and their mRNA was analyzed using oligonucleotide microarrays.
Keywords: time series design

overall_design: Cy3-labeled reference probes (untreated) and Cy5-labeled probes (samples exposed for the indicated times) were hybridized to 70-mer oligonucleotide microarrays with 21,329 probes (Qiagen Human Array-Ready Oligo Set, Version 2.0). The arrays were printed by the Advanced Technology Center at the National Cancer Institute. At least two hybridizations (range 2-5) were performed for each sample.


title: Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast

status: Public on Aug 11 2005

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

summary:
Genome wide roles for fission yeast HDACs
Keywords: Genome wide roles for fission yeast HDACs

overall_design: We have conducted a genome wide investigation into the enzymatic specificity, expression profiles, and binding locations of four histone deacetylases (HDACs), representing the three different phylogenetic classes in fission yeast (Schizosaccharomyces pombe). By directly comparing nucleosome density, histone acetylation patterns and HDAC binding in both intergenic and coding regions with gene expression profiles, we found that Sir2 (class III) and Hos2 (class I) have a role in preventing histone loss, Clr6 (class I) is the principal enzyme in promoter-localized repression. Hos2 has an unexpected role in promoting high expression of growth-related genes by deacetylating H4K16Ac in their open reading frames. Clr3 (class II) act cooperatively with Sir2 throughout the genome including the silent regions: rDNA, centromeres, mat2/3 and telomeres. The most significant acetylation sites are H3K14Ac for Clr3 and H3K9Ac for Sir2 at their genomic targets. Clr3 also affects subtelomeric regions which contain clustered stress and meiosis induced genes. Thus, this combined genomic approach has uncovered different roles for fission yeast HDACs at the silent regions in repression and activation of gene expression.

first: Marianna

last: Wirén

first: Rebecca

last: Silverstein

first: Indranil

last: Sinha

first: Julian

last: Walfridsson

first: Hang-mao

first: Patricia

last: Laurenson

first: Lorraine

last: Pillus

first: Daniel

last: Robyr

first: Michael

last: Grunstein


title: Expression Analysis of Gastric Cancers

first: Amit

last: Aggarwal

summary:
Microarray Expression profiles from 58 samples comprising of 3 normals and 55 gastric cancers is used for molecular subclassification of Gastric Cancers.

Data Generation and Processing:
The ratiometric data here is given by Ch1(Cy3)/Ch2(Cy5) where Ch2 is Universal Reference RNA from Stratagene. Two different chips were used (13K and 18k); The ratio metric is given by (Biological sample / Universal Reference). The Biological Samples are labeled with Cy3 (Green) and the Universal Reference RNA is always labeled with Cy5 (Red).

Two types of spots were excluded
a) Spots for which Foreground intensity was lower from background by lesser than 10 fluoresence units.
b) Spots that couldnt be identified reliably by the scanner (Arrayworx) software within the "region of interest" masked by the user.
The 2 channels for each array are equalized by multiplying the reference channel Ch2(Cy5) by a constant which is derived by (Total Cy3 / Total Cy5).

Subsequently, all expression ratios from each array is normalized to have median expression value = 1.
Keywords: other

first: Yu

last: Kun

first: Patrick

last: Tan


title: Drosophila HSF chromatin IP -cDNA array

status: Public on May 30 2005

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

summary:
Chromatin immunopurifications from heat shocked drosophila embryos with anti-Heat shock factor sera compared with immunopurification with pre-immune sera. Hybridisations to cDNA arrays.
Keywords: repeat sample

first: Steven

first: Robert

last: White

first: Ian

last: Birch-Machin

first: Shan

last: Gao

first: David

last: Huen

first: Richard

last: McGirr


title: SSc sera stimulated HDEC culture time course

status: Public on Jul 30 2005

first: Syed

middle: S

last: Ahmed

address: 715 Albany Street

department: Medicine

institute: Boston University School of Medicine

summary:
This series represents HDEC cultured in 10% control sera vs. SSc sera with ACA vs. SSc sera with SCL70
Samples were analyzed at 1, 6, 12, and 24 hours

The data that have been provided in the GEO Samples (GSMs) are from QuantArray.  The values indicated under the VALUE header were obtained by taking the log (base 2) of the ratio of the raw data from the experimental samples to the reference RNA samples.

These raw data were subsequently analyzed by Cluster and TreeView which normalizes the data across samples (see appended Table).  The normalization procedure was as follows:  Background corrected intensity expression levels were normalized per channel using the software program called Cluster as follows:  one cycle of log transformation, five cycles of median centering of genes, and five cycles of normalizing genes to generate a log-transformed, median polished, and normal (magnitudes close to 1.0) dataset.

Keywords = HDEC, SSc sera stimulation
Keywords: time-course


title: Expression profiling of rpb1-11

status: Public on May 01 2005

first: Karl

last: Ekwall

summary:
Two independent RNA preparations were used to hybridise to two microarrays one on
which wildtype was labelled with Cy5 and rpb-11 with Cy3 and the other on which dyes
were swapped.
The data were normalized using 'Lowess' (per chip per spot normalizations and checked
against luciferase spiking controls).
Using a 1.5 fold cutoff value for changes in expression levels 33 genes showed
reproducible up or down regulation, none of which are known to be involved in RNAidependent
transcriptional gene silencing.
The methodology and arrays were as previously described by Xue et al (2004).
Keywords: parallel sample

first: Vera

last: Schramke

last: Sheedy

first: Ahmet

last: Denli

first: Carolina

last: Bonilla

first: Gregory

last: Hannon

first: Robin

last: Allshire


title: Spotted Dick Chromatin Immunopurification

status: Public on May 07 2005

first: Andrew

middle: Robin

last: Page

summary:
Chromatin enriched by immunopurification with antibodies against the Drosophila transcription factor spotted dick compared with pre immune sera on a cDNA microarray
Keywords: parallel sample

first: Andras

last: Kovacs

first: Peter

last: Deak

first: Tibor

middle: T

last: Torok

first: Istvan

last: Kiss

first: Paulo

last: Dario

first: Chrisitna

last: Bastos

first: Pedro

last: Batista

first: Rui

last: Gomes

first: Hiro

last: Ohkura

last: Glover


title: Murine CD8+ Pmel Lymphocytes IL-2 vs. IL-15

status: Public on Apr 27 2005

first: Keith

last: Kerstann

department: Surgery Branch

institute: National Institutes of Health

summary:
Central memory tumor-reactive CD8+ T cells confer superior antitumor immunity compared to effector memory T cells
Keywords: other

first: Christopher

last: Klebanoff

first: Luca

last: Gattinoni

first: Parizad

last: Torabi-Parizi

middle: W

first: Adela

last: Cardones

first: Steven

middle: E

last: Finkelstein

first: Doug

last: Palmer

first: Paul

last: Antony

first: Sam

last: Hwang

last: Rosenberg

first: Thomas

last: Waldmann

first: Nicholas

middle: P

last: Restifo


title: Transcriptomic alterations induced by AT-EAE in mouse spinal cord

status: Public on Mar 26 2005

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary:
We compared RNA samples extracted from spinal cords of control (C) and AT-EAE (E) mice using the "Multiple Yellow" strategy. 4 distinct C-extracts were hybridized with two slides and 4 distinct E-extracts with other two slides, and the green/red normalized signals were compared separately and the E/C ratios averaged.
Keywords = white matter
Keywords = inflammation
Keywords = cDNA microarray
Keywords = experimental autoimmune encephalomyelitis

first: Elimor

last: Brand-Schieber

first: Peter

last: Werner

first: Sanda

first: Michelle

last: Beelitz

first: Stuart

last: Lowery

first: David

last: Spray

first: Eliana

last: Scemes


title: CEA_SGF:E00010#bcr-abl

city: Villejuif

first: Ali G.

last: Turhan

country: France

institute: institut Gustave Roussy

summary:
Chronic myelogenous leukemia (CML) is a malignant disease of the hematopoietic stem cell, characterized by the expression of the Bcr-Abl oncogene by leukemic cells. In order to analyze the molecular pathways modulated by Bcr-Abl, we have previously generated an inducible model of Bcr-Abl expression in the murine Ba/F3 cell line based on the Tet-OFF system. In the present study, through a microarray approach applied to cells grown with (Bcr-Abl-expression OFF) or without (Bcr-Abl-expression ON) doxycycline, a tetracycline analogue, we analyzed the gene expression variations upon Bcr-Abl expression.
Keywords: repeat sample


title: 30MPa, temp25,16h

status: Public on Apr 14 2005

city: Tsukuba

first: Hitoshi

last: Iwahashi

department: Human Stress Signal Research Center

institute: National Institute of Advanced Industrial Science and Techology

summary:
Series containes 4 independent experiments and high and low power scanns for each independent experiment.

Genome-wide mRNA expression profiles of Saccharomyces cerevisiae growing under hydrostatic pressure were characterized.  We selected a hydrostatic pressure of 30 MPa at 25°C because yeast cells were able to grow under these conditions, while cell size and complexity were increased after decompression.  Functional characterization of pressure-induced genes suggests that genes involved in protein metabolism and membrane metabolism were induced. The response to 30 MPa was significantly different from that observed under lethal conditions because protein degradation was not activated under 30 MPa pressure.  Strongly induced genes included those that contribute to membrane metabolism and which are also induced by detergents, oils, and membrane stabilizers.
Keywords: repeat sample

first: Mine

last: Odani

first: Emi

last: Ishidou

first: Emiko

last: Kitagawa


title: DOT4/dot4-1 and DOT4/dot4-5 transcript arrays

status: Public on Mar 31 2005

first: Daniel

last: Gottschling

address: 1100 Fairview Avenue N., Mailstop A3-025

department: Division of Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary:
Comparison of DOT4-6Myc/dot4-1-6Myc cells, DOT4-6Myc/dot4-5-6Myc cells, DOT4-6Myc/dot4 null cells, DOT4-6Myc/DOT4 cells in YEPD
Keywords: other

first: Richard

last: Gardner

first: Zara

last: Nelson


title: Pmel CD8+ stim 1 vs. stim 2

status: Public on Mar 02 2005

first: Keith

last: Kerstann

summary:
Repeat experiments of CD8+ pmel effector cells following one and two rounds of restimulation
Keywords: repeat sample

first: Luca

last: Gattinoni

first: Christopher

last: Klebanoff

first: Douglas

last: Palmer

first: Claudia

last: Wrzesinski

first: Zhiya

last: Yu

first: Steven

last: Finkelstein

first: Deborah

last: Surman

last: Rosenberg

first: Nicholas


title: 50 ppm Patulin treatment for 2 h

status: Public on Jul 13 2005

state: Ibaraki

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

summary:
Patulin, 4-hydroxy-4H-furo[3,2c]pyran-2(6H)-one, is one of the most popular and characterized mycotoxin observed in agricultural products. However the mechnisims of toxicity by this chemical is not well understood.  Thus, we characterized the cytotoxicity of patulin using yeast transcriptome systems.  The expression profile of mRNA after exposure yeast cells to patulin was similar to those after the treatment by antifungal agricultural chemicals such as thiuram, maneb, and zeneb.   The Patulin treatment activated protein degradation especially proteasome activities, sulfur amino acid metabolisms, and oxidative stress defense system.  DNA alkylation damages was also suggested and this seems to be repaired by recombinational and excision repair mechanism.  We also list the indicator genes for the detection of patulin in agricultura product.
Keywords: stress response

overall_design: Series containes 3 independent experiments and high and low power scanns for each independent experiment.

first: JiHyun

last: Park

first: JooHee

last: Lee


title: Intrathymic T-cell selection

status: Public on Mar 07 2005

first: Remy

last: Bosselut

institute: NCI, NIH

summary:
Comparisons between untreated primary cells T-cell precursors from the thymus. CD69- thymocytes are from Zap70-deficent mice and are >95% CD4+CD8+. These cells fail to generate intrathymic TCR signals as a result of their lacking Zap70 molecules, and are thus representative of "preselection" CD4+CD8+ thymocytes. The CD69hi population comes from wildtype mice and is heterogeneous for CD4 and CD8 expression. These cells have been intrathymically TCR-signaled and are undergoing selection.
Keywords: other

first: Guangping

last: Sun

first: Xiaolong

last: Liu

first: Rémy


title: Human TK6 cells treated with BPDE or N-OH-AABP yielding 5%, 15% and 40% of toxicity

first: Wen

last: Luo

address: 1800 East Lake

department: Human Biology

summary:
Cell culture
Human lymphoblastoid line TK6 was derived from the parental human lymphoblastoid line HH4 and heterozygous for thymidine kinase (TK), an enzyme which phosphorylates thymidine and its toxic analogs in an ATP-dependent reaction. The cells were grown in spinner flasks to allow for gentle stirring.  Cells were maintained in exponential growth by daily dilution in RPMI 1640 medium supplemented with 5% donor horse serum and maintained in 37oC incubators with a 5% CO2 atmosphere.  Cell counts were taken daily using a Coulter Counter, and cultures were diluted to 4~5´105 cells/mL.  Detailed growth records were maintained and used to ascertain any effects of the treatment on growth rate.

Chemical treatment, mutagenesis and survival measurements
N-OH-AABP and BPDE stock solutions were prepared in anhydrous DMSO (99.997% purity) and used immediately. The final DMSO concentration in the culture was less than 0.1%.

Prior to mutagen treatment, the background HPRT mutant fraction was reduced. TK6 cells were first “CHAT” treated for three days, followed by two days recovery period in “THC”.  Cells were then treated with various concentrations of test chemicals such as BPDE or N-OH-AAB for up to 27 hours. Duplicate cultures were completed at each condition. Untreated cells were used as negative controls. At the end of the treatment, cells were sampled for measurement of the mutant fractions, DNA adducts level and gene expression. At 1, 9 or 27 hours after the treatment, cells were sampled for mutant fraction.  At sampling, a 100 ml aliquot from each culture was centrifuged, and cells were resuspended in fresh RPMI medium to remove test chemicals. After cells had been growing exponentially for 7 days to allow for phenotypic expression, cultures were plated to determine mutant fractions. To determine mutant fraction at HPRT or TK locus, cells were plated in the presence and absence of 6-thioguanine (6TG) or triflurothymidine (F3TdR), respectively. The mutant fraction is the ratio of the colony-forming efficiency under selective conditions to that of efficiency in the absence of selective conditions. Survival of treated cultures was calculated from back extrapolation of growth curves by comparison of the growth of treated cultures to control cultures. For analysis of gene expression and DNA adducts, two 100 ml aliquots of cells (about 5´105 cells/mL) were removed from each culture at 1, 9 or 27 hours after the treatment. Cells were collected by centrifugation, immediately frozen down in liquid nitrogen, and stored at -80oC.

DNA microarrays
Human cDNA arrays were generated in the Genomics Facility at Fred Hutchinson Cancer Research Center. Microarrays were constructed employing the first 17,569 clones from the sequence-verified ResGen Human Unigene Set comprising 31,105 clones (Research Genetics, Huntsville, AL - now Invitrogen). Although each clone was originally representative of a unique UniGene Cluster, members of these clusters have changed over time. Our review of the annotations for 521 clones indicated that redundancy of probes was approximately less than 2.5% (12/521). Clones are representative of over 20 different human tissues/organs.  The average length of the probe was 1200 ± 364 bases, with the minimum probe length being 251 bases and the maximum probe length being 2000+ bases.

For array construction, each clone insert was individually amplified using PCR. Each PCR product was then verified on the basis of size using gel electrophoresis, and purified using the Millipore Multiscreen-PCR filtration system. In some instances, re-sequencing was performed to verify the identity of clones. Purified PCR products in 3X SSC (450 mM sodium chloride and 45 mM sodium citrate, pH 7.0) were each mechanically “spotted” onto poly-lysine coated microscope slides using an OmniGrid high-precision robotic gridder (GeneMachines, San Carlo, CA).  Each clone was represented once per array.

Preparation and hybridization of cDNA probes labeled with Cy3 or Cy5

RNA was extracted using Qiagen RNeasyMaxi Kits according to the manufacturer’s instructions (Qiagen, Valencia, CA), followed by a quality test using Agilent BioAnalyzerächips. Synthesis of the labeled first strand cDNA was conducted using InVitrogen Superscript II reverse transcript system with starting material of 30 µg total RNA plus oligo-dT. The amino-allyl labeled dUTP was added to the reaction to generate amino-allyl labeled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using a Microcon–30 concentrator. Probe mixtures were evaporated in a vacuum centrifuge, and the cDNA pellet was resuspended in 4.5 µL of water. The dye coupling reactions were performed by mixing the cDNA samples with Cy3 or Cy5 dyes and incubating for 1 hour in the dark. After the reactions were quenched with hydroxylamine, Cy3 and Cy5 samples were combined for hybridization. To remove unincorporated/quenched Cy dye, a Qia-quick PCR purification kit (Qiagen) was used. The reactions were purified with Qiaquik PCR purification kits to remove the unincorporated/quenched dyes. The mixture of Cy3 and Cy5 labeled samples was dried down in a vacuum centrifuge and then brought to a volume of 20 µL with water. Millipore 0.45 µM spin columns were used to clean up after adding 20X SSC and Poly A to the mixture. Finally, the samples were stored at –20o C until ready for hybridization.

The labeled cDNAs were co-hybridized to cDNA microarrays in triplicate, including one dye swap. Slides were scanned on the GenePix 4000A Microarray Scanner at the optimal wavelength for the Cy3 and Cy5 using lasers. The fluorescence signals of each spot on the slide were analyzed and extracted with GenePix software to generate .gpr file, which was further formatted to plain .txt file for further data analysis. All the data mining steps including transformation, cleaning-up, normalization and hypothesis tests, were performed using the SAS statistical software.

Keywords: repeat sample

first: Wenhong

last: Fan

first: Hong

last: Xie

first: Lichen

last: Jing

first: Elaine

last: Ricicki

first: Paul

last: Vouros

first: Lue Ping

last: Zhao

first: Helmut

last: Zarbl


title: (ratio exp) LAT3YF CD5+ gamma delta T cells

status: Public on Mar 01 2005

first: Hans-Joachim

last: Mollenkopf

summary:
ratio experiment by combining dye-reversal ratio profiles

CD4+ alpha beta T cells were positively sorted from LatY136F or from wild-type spleen using a MACS and anti-CD4 beads. Gamma delta T cells were sorted from the spleen of Lat3YF and of Eb-/- mice using MACS and anti-CD5 beads. In vitro differentiated Th1 and Th2 cells were generated by culturing naive wild-type CD4+ T cells for 4 days in complete RPMI in the presence of anti-CD3 (1 µg/ml) plus anti-CD28 (1 µg/ml) with the addition of IL-12 (10ng/ml) and of anti-IL-4 (5µg/ml) for Th1-polarizing conditions, and of IL-4 (20ng/ml) plus anti-IFN-gamma (10µg/ml) for Th2-polarizing conditions. RNA was prepared using the Trizol method followed by DNAse digestion.
Microarray experiments were carried out as two-color ratio hybridizations. RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, cDNA was reverse transcribed from 4 µg total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with either cyanine 3-CTP (Cy3-CTP) or cyanine 5-CTP (Cy5-CTP) and T7 polymerase. The fluorescent-labeled antisense cRNA was precipitated over night with LiCl, ethanol washed and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP and A650nm for Cy5-CTP and labeling efficiency was verified with a Nanodrop photometer (Kisker, Steinfurt, Germany). Before hybridization, 1.25 µg labeled cRNA of each product were fragmented and mixed with control targets and hybridization buffer according to the supplier's protocol (Agilent Technologies). Hybridizations were done over night for approximately 17 h at 60°C. The slides were washed according to the manufacturer's manual and scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies). In order to compensate dye specific effects, and to ensure statistically relevant data, a color swap dye reversal was performed. Features were extracted with an image analysis tool Version A 6.1.1 (Agilent Technologies) using default settings. Data analysis was carried out on the Rosetta Inpharmatics platform Resolver Built 4.0. Expression patterns were identified by stringent data analysis using anti-correlation of the dye reversal ratio profiles and a 2fold expression cut-off of the ratio experiments. By combining the first and the second criteria of analysis we filtered out data points with low P-value (P-value < 0.01), making the analysis robust and reproducible. Additionally, by using this strategy we did the data selection independent of error models implemented in the Rosetta Resolver system.
Keywords: other

first: Immo

last: Prinz


title: (ratio exp) LATY136F CD4+ alpha beta T cells


title: Differential Gene Up-regulation by HIF-1a and HIF-2a in HEK293T.

status: Public on Apr 01 2005

first: Victoria

last: Wang

institute: NCI

summary:
Cell lines. HEK293 human embryonic kidney cells were obtained from ATCC (American Type Culture Collection, Manassas, VA) and were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Heat inactivated, Hyclone, Logan, Utah) and 1X antibiotics/glutamine (100 units/ml penicillin, 100ug/ml streptomycin, 292ug/ml L-Glutamine sulfate, all from Invitrogen Corp, Carlsbad, CA.), under either hypoxic (1% O2) or normoxic (21% O2) conditions at 37C in a tissue culture incubator.

Treatment. Cells treated in hypoxia for 16 hours or transfected with HIF-1a (HIF-1amut or HIF2a) plasmid. At the end of treatment, cells were collected and washed.

Microarray studies.  Total RNA samples were extracted from HEK293T cells grown in 1% or 21% O2 overnight and from transfected cells. Total RNA (20 µg) from each sample was synthesized into double-stranded cDNA with reverse transcriptase (Fairplay labeling kit, Stratagen, La Jolla, CA) using an oligo d(T) primer. The double stranded cDNA from untreated cells was labeled with Cy3 monofunctional reactive dye and that from hypoxia-treated or transfected cells was labeled with Cy5 monofunctinal reactive dye. The probe was hybridized to a long oligo array (Hs-Operon V2-vB1.1px.gal) containing 20K human transcripts (NCI Microarray Facility, Advanced Technology Center, Gaithersburg, MD) overnight at 42C . The slides were washed and spin-dried. Microarray slides were scanned with a GenePix 4000 microarray scanner (Axon Instruments, Union City, CA.).  The microarray images were analyzed with GenePix 3.0 software and data analysis was performed with the MicroArray Database (mAdb) system hosted by the Center for Information Technology and Center for Cancer Research at the NCI.
Keywords: other


title: DOT4/dot4 null, UBP8/ubp8 null transcript arrays

status: Public on Feb 25 2005

first: Daniel

last: Gottschling

summary:
Comparison of DOT4/dot4 null cells, UBP8/ubp8 null cells, and DOT4UBP8/dot4ubp8 null cells in YEPD.
Keywords: other

first: Richard

last: Gardner

first: Zara

last: Nelson


title: Normal_human_tissues_genomic_controls

status: Public on Feb 21 2005

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

summary:
Array hybridizations profiling diverse human tissues; for each array the human tissue RNA is hybridized against a universal reference RNA. Experiments 1-3 are replicates of universal reference RNA vs. genomic DNA hybridizations, used to estimate transcript abundance. Arrays 4-8 are tissue RNA vs. genomic DNA hybridizations, carried out to evaluate the method for estimating transcript abundance (see manuscript for details).
Logical set
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: other

first: Young

last: Kim


title: (dye reversal) wildtype CD4+ alpha beta T cells vs. LATY136F CD4+ alpha beta T cells

institute: Max-Planck-Institute for Infection Biology

summary:
color swap ratio profiles

(dye-reversal) wildtype CD4+ alpha beta T cells vs. LATY136F CD4+ alpha beta T cells: GSM42565 and GSM42566
Keywords: repeat sample


title: Differential Gene Expression due to direct effects of IL-13 on Airway Epithelial Cells

status: Public on May 27 2005

city: San Francisco

first: Michael

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

summary:
This series represents the effects of OVA, tg-IL-13, and direct effects of IL-13 on airway epithelial cells.

Experiment Design:

Type of experiment: comparison of three related murine models of asthma, 1) Ova model, 2) tg-IL-13 model, 3) IL-13/Epi model. Two control groups were used: PBS challenged mice to control for the effects of OVA and tg-IL-13+ and STAT6-/- mice as controls for tg-IL-13 and IL-13/Epi mice. Measurements were made in each model in two types of tissue samples, whole lung and tracheal perfusate.

Experimental factors: Allergen vs sham challenge, natural STAT6 expression vs transgenic expression and no expression.

The number of hybridizations performed in the experiment: 50 (25 whole lung and 25 tracheal perfusate).

The type of reference used for the hybridizations, if any: Pooled reference from lung (whole lung or tracheal perfusate) from untreated wildtype mice.

Hybridization design: two-color hybridizations with reference design. Each individual sample was hybridized to a separate array.

Quality control steps taken: 5 experimental replicates per group. RNA integrity assessed by Agilent Bioanalyzer. Arrays with low signals, high background, or high spatial variation rejected and corresponding samples reanalyzed.

URL of any supplemental websites or database accession numbers:GEO (http://www.ncbi.nlm.nih.gov/geo, accession number GSE1438).

**********

Samples used, extract preparation and labeling:

The origin of the biological sample: homogenized whole lung from mouse and perfusate of mouse trachea.

Manipulation of biological samples and protocols used: Whole lungs mechanically homogenized in 7.0 ml Trizol reagent (Invitrogen) for total RNA collection. Tracheas perfused with lysis buffer (Qiagen Rneasy kit) for total RNA collection.

Protocol for preparing the hybridization extract and labeling: Preparation of aminoallyl-UTP labeled whole lung cDNA was performed as described [1]. Total RNA from tracheal perfusate (1.0 - 1.5 g per sample) was amplified and labeled with aminoallyl-dUTP using the MessageAmp aRNA kit (Ambion). Labeled cRNAs were coupled to Cy3 or Cy5 dyes (CyScribe, Amersham Biosciences) and purified as described [1].

Labeling protocol(s): Coupled to Cy3 or Cy5.External controls (spikes): none.

**********

Hybridization procedures and parameters:

Hybridizations were performed as described [1] except Ambion SlideHyb Glass Array Hybridization Buffer #1 (neat concentration) was used as hybridization buffer and hybridizations were carried out for 40 h at 55 °C.  Following hybridization, arrays were washed in 1X SSC with 0.03% SDS (wash 1), 0.2X SSC (wash 2), and 0.05X SSC (wash 3) for five minutes for each wash.

**********

Measurement data and specifications:

Arrays were scanned using an Axon Genepix 4000B scanner and GenePix Pro Analysis 5.0 software; laser power 100%, 10 micron resolution, PMT optimized for each array. Data from GPR files are available from GEO (http://www.ncbi.nlm.nih.gov/geo, accession number GSE1438).The “print-tip loess” normalization was used to correct for within-array dye and spatial effects and single channel quantile normalization was used to facilitate comparison between arrays. No background subtraction was performed. We used functions in the library marrayNorm of the R / Bioconductor package to perform these normalizations. After normalization we determined the log2 ratio of experimental sample intensity to reference sample intensity for each probe on each array.

**********

Array Design:

General array design

Array design name: UCSF 10Mm Mouse v.2 Oligo Array (GEO GPL1089) and UCSF Gladstone 18K Mouse v.2 Oligo Array (GPL1196)

Platform type: spotted oligonucleotides (70mers)

Surface and coating specification: aminosilane coated glass slides

Physical dimensions of array support (e.g. of slide): 25 x 75 x 1.0 mm

Number of features on the array: GPL1089: 19152, GPL1196: 18240 (including empty and duplicate features)

For production protocol, see http://www.microarrays.org/pdfs/PrintingArrays.pdf

Feature information is available from GEO (GSE1438).

Reporters: synthetic single stranded oligonucleotides. Sequence and annotation information available from GEO (GPL1089 and GPL1196)

Method of reporter preparation: synthesized by Operon.

The spotting protocols used, including the array substrate, the spotting buffer, and any post-printing processing, including cross-linking: see http://www.microarrays.org/pdfs/PrintingArrays.pdfAny additional treatment performed prior to hybridization: none.

**********

Reference:

1.	Barczak A, Rodriguez MW, Hanspers K, Koth LL, Tai YC, et al. (2003) Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res 13: 1775-1785.
Keywords = IL-13
Keywords = Epithelial
Keywords = differential gene expression
Keywords = microarray
Keywords: parallel sample

first: Douglas

last: Kuperman

first: David

middle: J

last: Erle


title: Normal_human_tissues

summary:
Array hybridizations profiling diverse human tissues; for each array the human tissue RNA is hybridized against a universal reference RNA.

Series_type: Logical set
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: other

first: Radha

last: Shyamsundar


title: Effects of Voluntary Exercise on Hippocampal Gene Expression in male C57Bl/6J mice

status: Public on May 26 2005

city: Baton Rouge

first: Leslie

middle: DeBardeleben

last: McLaughlin

state: LA

address: 6400 Perkins Road

department: Department of Experimental Obesity

institute: Pennington Biomedical Research Center

summary:
This experiment was designed to identify changes in gene expression in the brain (specifically the hipocampus) in relation to variable levels of voluntary exercise.  Male C57Bl/6J mice were weaned onto a low fat diet (LF; Research Diets D12329, 11% kcal fat) and given continuous access to exercise wheels (30.3 x 20.6 x 26 cm; Mini Mitter®, Nalgene® Activity Wheel for Rodents) at ten weeks of age, for three days (n=96). Six mice had their wheels locked to act as sedentary controls (sed).  Animals were considered to be high runners (HR) if they ran >= 5 km/night and low runners (LR) if they ran <= 2 km/night.  Middle runners (MR) were chosen randomly from the population of animals falling between the high and low groups.  This series is comprised of array results from three parallel experiments comparing HR versus sed, MR versus sed, and HR versus LR.  Six hybridizations were performed for each of the three comparisons (3 forward-labeled, 3-reverse labeled) to account for dye-incorporation differences.  One slide from the HR vs LR experiment was broken during processing, so only five are included from that group.
Keywords = hippocampus
Keywords = voluntary running
Keywords = voluntary exercise
Keywords = C57Bl/6J
Keywords: parallel sample

middle: D

first: Christopher

last: Faulk


title: A distinct and unique M2 transcriptional program expressed by tumor-associated macrophages

status: Public on Jan 31 2005

city: Frederick

first: Lisa

middle: M

last: Gangi

address: 915 Tollhouse Ave

department: LMT-Frederick

summary:
Description This series contains microarrays for tumor associated macrophages (TAMs) purified from 8 week old male C57/BL6N mice, 3 weeks after tumor implantation into the left hind limb. Peritoneal exudates cells (PECs) were also harvested from control C57/BL6N mice. The resulting adherent populations were maintained in culture and resting TAMs and PECs were treated for 4 hours with 100 ng/mL of LPS to promote macrophage activation.

RNA isolation and cDNA microarrays: Total RNA was isolated from approximately 20x10e6 PEC and TAM cells using standard Trizol purification protocols (Invitrogen, Carlsbad, CA). Microarrays were manufactured at the NCI, Laboratory of Molecular Technology (Frederick MD). The 10,368 Mm UniGem2 set was printed on poly-lysine coated glass slides and hybridized according to NCI facility protocols. All slides were scanned using as Axon GenePix 4000 scanner (Axon Instruments, Foster city, CA) and resulting data was uploaded for analysis to the mAdb microarray database (http://madb.nci.nih.gov/).
Keywords = tumor associated macrophage
Keywords: other

first: S

last: Biswas

first: L

first: T

last: Schioppa

first: A

last: Saccani

first: P

last: Saki

first: M

last: Sironi

first: B

last: Bottazzi

last: Mantovani

last: Sica


title: Erythroid differentiation: Murine erythroleukemia cell induction

status: Public on Feb 01 2005

city: University Park

first: Ross

last: Hardison

state: PA

department: BMB

institute: The Pennsylvania State University

summary:
Transcriptional profiling of murine erythroleukemia cells induced to differentiate

Murine erythroleukemia (MEL) cells are derived from mice infected with the Friend erythroleukemia viral complex, which causes a lethal expansion of erythroid cells. The transformed, immortalized cells (MEL cells) isolated from infected mice are committed to erythroid differentiation, but are blocked roughly at the proerythoblast stage. Treatment with small, oxidized organic compounds like dimethyl sulfoxide or hydroxymethyl-bis-acetamide (HMBA) induce the cells to mature further, to roughly the erythroblast stage or beyond in some lines  (Friend et al. 1971). During this induction, the amount of hemoglobin, some heme biosynthetic enzymes and other proteins characteristic of mature erythroid cells increases, largely as a result of changes in transcription (Aviv et al. 1976). A full description of changes in transcription of all mouse genes during this process is not available.

To improve this situation, we have conducted transcriptional profiling of the RL5 line of MEL cells, using microarrays containing almost 7000 mouse genes. The RL5 line has a "random locus" containing a positive-negative selectable marker (HyTK) flanked by loxP sites, thus facilitating site-directed integration into the cells (Bouhassira et al. 1997; Feng et al. 1999; Molete et al. 2001). This particular line is not highly inducible, with less than half the cells accumulating large amounts of hemoglobin. However, they are advantageous for integration of expression constructs, which is our particular interest.

MEL_RL5 cells were treated with 4 millimolar HMBA for 6 days to induce maturation, and RNA was isolated each day. Complementary DNA was synthesized and labeled with either Cy5 (red fluorescence) for the induced samples or Cy3 (green fluorescence) the untreated cells grown in parallel. For most time points, at least two independent experiments were run, some with dyes switched (SD). The microarrays were spotted at the PSU Microarray Facility. Hybridization was carried out in our laboratory, and hybridized chips were scanned on a GenePix scanner and quantified using GenePix software. The signals from each channel (red and green) were normalized so that the total red intensity equals the total green intensity.

Data were filtered to remove "bad" spots, which are those in which the noise exceeded the signal. We calculated the median of the pixel intensities for each spot and standard deviation around the median, and with these values we computed a "modified Z-score" for each channel on each spot. A lenient threshold for the "modified Z-score" was applied to remove "bad" spots.

After filtering, we performed global mean normalization for each chip, followed by lowess normalization for each chip to remove intensity-dependent effects.

Keywords: time-course


title: Drug treatment comparison

status: Public on Jan 27 2005

city: Seoul

first: Se Nyun

last: Kim

country: South Korea

institute: Digital Genomics, Inc.

summary:
H460 cells were treated with 5-FU, cytarabin, cisplatin, paclitaxel, and cytochalasin D.  Gene expression changes induced by drug treatment were compared.
Keywords: other


title: SAN1/san1 YEPD/YC transcript arrays

status: Public on Jan 19 2005

first: Daniel

last: Gottschling

summary:
comparison of SAN1/san1 cells in YEPD and YC
Keywords: other

first: Richard

last: Gardner

first: Zara

last: Nelson


title: Mouse Expression DB 2001 CHMC

status: Public on Jan 25 2005

city: Cincinnati

first: Bruce

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

summary:
Expression profiles of different mouse tissue samples
profiles.
Keywords: other

first: Joanna

middle: A

last: Groden

first: Mitchell

last: Cohen

first: Michael

last: Bates

first: Dan

last: Wiginton

first: Chris

last: Erwin

first: Kathleen

last: Anderson

first: Sandra

last: Degen

first: Susan

last: Waltz

first: Belinda

last: Peach

first: Thomas

last: Doetschman

first: Jeff

last: Molkentin

first: Jonathan

last: Katz

first: Steve

last: Potter

first: Jorge

last: Bezerra

last: Mucenski

first: James

last: Lessard

first: MaryBeth

last: Genter

first: Amy

last: Moseley

first: Jianhua

last: Zhang

last: Lehman

first: Ming

last: Xu

first: John

last: Maggio

first: Linda

last: Parysek

first: R

last: Hirsch

last: Dedman


title: 2091 mock vs. 2091 E2F4 IP - Human 13K

status: Public on Jan 01 2005

city: Boston

first: Jonghwan

last: Kim

address: 1 Blackfan circle Karp-7

institute: HMS/CHB

summary:
2091 mock vs. 2091 E2F4 IP - Human 13K promoter microarray

2091 cells were serum starved for 72hours and fixed with formaldehyde.
Keywords: repeat sample


title: Rosetta_miRNA_transfection_experiment

city: Seattle

first: Lee

last: Lim

institute: Rosetta Inpharmatics

summary:
This series consists of samples taken from HeLa cells transfected with one of 7 (wild-type or mutant) miRNA duplexes and harvested either 12 or 24 hours later.
Submitted for Nature publication Lim et al.
Keywords = microRNA
Keywords: other

first: Nelson

middle: C

last: Lau

first: Philip

last: Garrett-Engele

first: Andrew

last: Grimson

first: Janell

last: Schelter

last: Castle

first: David

last: Bartel

first: Peter

last: Linsley

first: Jason

last: Johnson


title: dmyc overexpression 7h and 14h

status: Public on Dec 16 2004

first: Ling

last: Li

address: 1100 Fairview Ave. N.

department: Basic Sciences

summary:
Fly strains: All transgenes are P[+] in w  strains. w+;+;Act 5c > CD2 > GAL4 UAS-GFP (Neufeld et al. 1998 ); y w hs-FLP122; +; UAS-dMyc (Zaffran et al. 1998 ). y w hs-FLP122; +; +. Adult flies and larvae were raised in regular fly food consisting of cornmeal and molasses at 25°C. Larvae overexpressing either UAS-regulated dMyc;GFP or GFP alone transgenes were generated using the Flp/Gal4 method (Struhl and Basler 1993 ; Pignoni and Zipursky 1997 ; Neufeld et al. 1998 ). Larvae were staged from hatching and raised at a density of 50 per vial at 25°C. Third instar larvae (110 h after egg deposition, AED) were heat shocked at 37°C for 2 h, and larvae were collected 7 h after heat shock (~120 h AED). Total RNA was isolated using TRIzol reagent (Invitrogen) as described by manufacturer followed by RNeasy (Qiagen) clear up. cRNA targets were generated using a standard amino-allyl labeling protocol, where 30 µg each of "experimental" (dMyc;GFP: hs-FLP122; Act-GAL4, UAS-GFP; UAS-dMyc) and "reference" (GFP only :ywhs-FLP122; Act-GAL4, UAS-GFP; +) total RNAs were coupled to either Cy3 or Cy5 fluorophores. Paired labeled targets were processed on microarrays using protocols described elsewhere (Fazzio et al. 2001 ). Posthybridized arrays were scanned using a GenePix 4000 scanner (Axon Instruments). Data were generated from five independent replicates (two with one dye orientation and three with the reversed dye orientation) at 7h and 14h
Keywords: repeat sample

first: Savraj

last: Grewal

first: Amir

last: Orian

first: Robert

middle: N

last: Eisenman

first: Bruce

last: Edgar


title: NIAID Mouse Lymphoma Gene Expression Profiling

status: Public on Dec 01 2004

city: Rockville

first: Jeff

middle: X.

last: Zhou

address: 5640 Fishers Lane

department: NIAID

institute: NIH

summary:
This series contains microarrays for ten types of mouse lymphomas, nude mouse purified resting B cells, and nude mouse purified B cells stimulated with LPS.  Microarray chips containing 70-mer oligonucleotides representing approximately 6,800 genes were prepared by the Microarray Center of the National Institute of Allergy and Infectious Diseases, Bethesda, MD.
Keywords = mouse
Keywords = lymphoma
Keywords = B cells
Keywords: other

first: Herbert

last: Morse

first: Thomas

last: McCarty

first: Windy

middle: F

last: Davidson

first: Zohreh

last: Naghashfar

middle: X


title: Hearts_tissue_expression_profile_3

status: Public on Dec 14 2004

city: Palo Alto

first: Svetlana

last: Shchegrova

institute: Agilent Technologies, Inc

summary:
Expression profiles in Adult Heart and Fetal Heart normal tissues.
Keywords: other


title: Effect 14-3-3 mutation on mRNA levels in yeast.

city: Leiden

first: Paul

last: van Heusden

address: Wassenaarseweg 64

country: Netherlands

institute: Institute of Biology

summary:
Studies on the effect of a bmh2 mutation on the genome-wide steady-state mRNA levels in Saccharomyces cerevisiae.
Keywords: other


title: Connexin43 null vs wildtype neonatal mouse HEART

status: Public on Nov 13 2004

first: Dumitru

last: Iacobas

institute: Prairie View A&M University

summary:
Cy3-labeled cDNA obtained from four pools of three hearts of neonatal C57BL Cx43 null mice were compared to Cy3-labeled cDNA obtained from four pools of three hearts of neonatal C57BL wildtype mice through Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.
Keywords = Cx32 null vs wildtype neonatal mouse heart
Keywords: parallel sample

first: Sanda

first: Wei

first: Georg

last: Zoidl

first: Rolf

last: Dermietzel

last: Spray


title: BIM1 synthetic lethality

status: Public on Nov 05 2004

city: Baltimore

first: Xuewen

last: Pan

address: 733 N. Broadway, Room 331

department: Department of Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary:
Assessment of synthetic lethality between a bim1 null mutation and Yeast Deletion mutations
Keywords = BIM1
Keywords = yeast
Keywords = deletion
Keywords = synthetic lethality
Keywords = tag
Keywords = barcode
Keywords: repeat sample

first: Daniel

middle: S

last: Yuan

first: Dong

last: Xiang

first: Xiaoling

last: Wang

first: Sharon

last: Sookhai-Mahadeo

first: Joel

last: Bader

first: Philip

last: Hieter

first: Forrest

last: Spencer

first: Jef

last: Boeke


title: Starvation response in Drosophila and its implication for sex specific metabolism and aging

status: Public on Nov 01 2004

city: Karlsruhe

first: Michael

middle: J.

last: Pankratz

department: Institute of Genetics

institute: Forschungszentrum Karlsruhe

summary:
Background
All animals must be able to adapt to changes in nutrient quality and supply. One striking aspect of this adaptive response is the extension of lifespan when caloric intake is reduced. These animals are also more resistant to various stresses, including starvation. We have characterized the response of adult Drosophila males and females to starvation and sugar conditions using high density microarrays.

Results
We have organized the regulated genes into specific metabolic and physiologic pathways. Most of the highly regulated genes have a strong sex bias. In addition to expected sex specific changes, such as egg production in females, we found unexpected biases in sensory systems, amino acid and purine metabolism, and signaling pathways. Comparison of starvation to caloric restriction revealed numerous overlaps.

Conclusions
Our results support the notion that starvation response shares similarities to caloric restriction. They have relevance for sex specific differences in longevity and in response to nutrient conditions which alter lifespan.

Nutrient Conditions and Fly handling
Larvae were kept on apple juice agar plates with yeast, and the larvae were raised at 25°C. For the developmental control larvae were collected 39-41 h AEL, for the developmental time-points at 51-53 hours and every 12 hours until 99-101 hours. Adult flies were kept at 25°C in 50 ml PS-tubes flat bottom (Greiner bio-one, Frickenhausen, Germany) on standard fly food (16.5 g yeast, 81,5 g cornmeal, 8 g agar, 100 ml sugar beet sirup and 200 ml 10% Nipagin in EtOH). Flies were collected that had hatched in 24 hours and kept in groups of ~200 flies/tube. After 5 days we separated males and females and put them in groups of 80/28 ml PS-tube. We allowed for one day CO2 recovery on standard fly food before flies were moved to 1) tubes with yeast paste on PBS soaked filter paper (control) 2) tubes with only PBS soaked filter paper (starvation) or 3) tubes with filter paper soaked in PBS with 20% Sucrose (sugar). After 24 or 48 hours flies were shock frozen in liquid nitrogen and stored at - 80°C for further handling.

Males and females were assayed separately. For females, we performed 24 and 48 starvation, and 24 and 48 hours sugar. For the males only 24 hour starvation was done, since most died upon 48 hour starvation; and 24 and 48 hour sugar. Briefly, flies were collected within a 24 hour period, allowed to stay together for 4 days, separated into males and females, and allowed one day recovery in normal fly food. Afterwards, the flies were placed into three conditions: fresh yeast plus PBS, PBS or PBS plus 20 % sucrose. These experiments essentially parallel the experimental set up of previous larval experiments (7). The starvation and PBS were then compared with yeast (control).

Keywords: ordered

first: Joerg

last: Katzenberger

first: Matthias

last: Bauer

first: Anne

last: Hamm


title: dSLAM

summary:
These datasets use diploid-based synthetic lethality analysis on microarrays (dSLAM) as a new technology for identifying genetic interactions of various types. These interactions include synthetic lethality (CIN8, BIM1, SGS1), synthetic haploinsufficiency (TUB1), dosage suppression (LCD1), suppression of a lethal mutation (SML1), suppression of an overexpressed conditionally lethal allele (CDC102), and gene-chemical interactions (Benomyl).
Keywords = dSLAM yeast heterozygotes barcode tag synthetic lethality suppression
Keywords: other


title: SGS1 synthetic lethality

summary:
Assessment of synthetic lethality between an sgs1 null mutation and Yeast Deletion mutations
Keywords = SGS1
Keywords = yeast
Keywords = deletion
Keywords = synthetic lethality
Keywords = tag
Keywords = barcode
Keywords: repeat sample


title: Irradiated vs sham irradiated keratynocytes

city: EVRY

first: Michèle

middle: T

last: Martin

address: 2, rue Gaston Crémieux

department: DSV/DRR

institute: CEA

summary:
CEA_SGF:E00006#
This set of experiments was performed in order to identify radiation responsive genes. For this, differentiated cultures derived from a single donor were irradiated at either 1 cGy, 2 Gy or sham-irradiated at T0 and total RNA extracts were prepared at 6 time points post-irradiation. Irradiated samples for each dose were hybridized seperately with sham-irradiated samples at the same time point. Each time point for each individual dose was assessed with two independent dye-swap hybridizations.
Keywords: time-course


title: Mouse Hepatocellular Carcinoma Study

status: Public on Oct 28 2004

city: Bethesda

first: Snorri

last: Thorgeirsson

address: 37 Convent Dr. # 4146

department: Laboratory of Experimental Carcinogenesis

institute: National Cancer institute/NIH

summary:
Genetically modified mice have been extensively used for analyzing the molecular events that occur during the tumor development. However, in many cases, if not all, it is uncertain to what extent the mouse models reproduce features observed in the corresponding human conditions. This is due largely to lack of precise methods for direct and comprehensive comparison at the molecular level of the mouse and human tumors. We used global gene expression patterns of 68 hepatocellular carcinoma (HCC) from 7 different mouse models and 91 human HCC from pre-defined subclasses to obtain direct comparison of the molecular features of mouse and human HCC.  Total RNAs were isolated from frozen liver tissue using CsCl density gradient centrifugation methods. Total RNA from the livers of 10 wild type mice were pooled and used as reference in entire microarray experiments. To obtain gene expression profile data from four transgenic HCC mouse models, 20 μg of total RNAs from tissues were used to drive fluorescently (Cy-5 or Cy-3) labeled cDNA. At least two hybridizations were carried out for each tissue using dye-swap strategy to eliminate dye labeling bias.
Keywords: other

first: Ju-Seog

last: Lee

first: I

last: Chu

first: A

last: Mikaelyan

first: D

last: Calvisi

first: J

last: Heo

middle: K

last: Reddy


title: CHIP Analysis - c-Jun/ATF2

status: Public on Oct 06 2004

city: San Diego

first: Yipeng

last: Wang

institute: Vaccine Research Institute of San Diego

summary:
Identification of promoters bound by c-Jun/ATF2 during rapid large-scale gene activation following genotoxic stress
Keywords: other

first: Jun

last: Hayakawa

first: Shalu

last: Mittal

first: Kemal

last: Korkmaz

first: Eileen

last: Adamson

first: Christopher

last: English

first: Masahide

last: Omichi

last: McClelland

first: Dan

last: Mercola


title: CEA_SGF:E00011#FGF6_effect

status: Public on Oct 01 2004

city: Evry

first: Geneviève

last: Piétu

summary: By using Hoechst staining techniques, we have previously shown that the C2C12 myogenic cell line contains a Side Population (SP) (Benchaouir et al, Exp Cell res, 2004) which is largely increased in the presence of FGF6 (Israeli et al, J Cellular Physiol, 2004). The experiment, compared transcriptional profiles from SP and MP (Main Population) cells from either C2C12 or FGF6-expressing C2C12.


title: Sham-irradiated vs pool of sham-irradiated keratinocytes

last: Martin

summary:
CEA_SGF:E00007#
This set of experiments was made in order to perform time series analyses. RNAs from sham-irradiated cells at each time point were pooled together. We then hybridized sham-irradiated samples at each time point versus cDNAs obtained from the pooled RNA. Each time point was assessed with two independent dye-swap hybridizations.
Keywords: time-course


title: Hearts_tissue_expression_profile

status: Public on Dec 10 2004

first: Svetlana

last: Shchegrova


title: Gene Expression Profile of NHE1 Null Mutation

status: Public on Jul 29 2004

city: La Jolla

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

summary:
Effect of NHE1 null mutation on gene expression in different brain regions
Keywords = NHE1 null mutation
Keywords = gene expression
Keywords = microarray
Keywords = brain
Keywords = mouse
Keywords: other

first: Jin

last: Xue

first: Orit

last: Gavrialov

first: Gabriel

middle: G

last: Haddad


title: Host Cell Gene Expression During HIV-1 Latency and Reactivation

status: Public on Aug 16 2004

first: Vyjayanthi

last: Krishnan

address: 10 Center Lane

department: HIV and AIDS Malignancy Branch

institute: NCI

summary:
Cells: ACH-2, and A3.01, were obtained through the NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH. ACH-2, is a chronically infected cell line harboring HIV-1 LAV strain, while A3.01 is the corresponding parental uninfected cell line.  Cells were grown in RPMI-1640 (Invitrogen, San Diego, CA) with 10% fetal bovine serum (FBS, Invitrogen), 5% penicillin-streptomycin (Invitrogen), and 2mM glutamine (Invitrogen).  Cells were maintained at a concentration of 1x10e6 cells/ml in T-175 flasks. Cell concentrations and cell viability were monitored throughout the experiment at all time points studied.  Cells were induced by addition of 20 ng/mL of phorbol myristyl acetate (PMA or TPA, Sigma, St Louis, MO) for one hour, after which the cells were washed with phosphate buffered saline (PBS).  Cells were harvested by centrifugation at 1000 rpm for 10 minutes, at the following times after induction, 0.5, 3, 6, 8, 12, 18, 24, 48, 72, and 96 hour(s).  HIV-infected and uninfected cells maintained and harvested in parallel with the PMA-treated cells, but not induced with PMA ( No PMA)were also harvested. Harvested cells were washed thrice with ice-cold PBS to remove media; cell pellets were snap frozen using ethanol-dry ice mixture and stored at (80°C for subsequent RNA extraction.
Total RNA Extraction:  Total RNA was extracted using RNEasy Midiprep Kits per manufacturer's protocol (Qiagen, Valencia, CA).  RNA concentrations and purity were measured by spectrophotometry, RNA quality (absence of RNA degradation) was assessed by gel electrophoresis.  RNA concentration was adjusted to the levels required for subsequent microarray experiment protocols by concentration in a SpeedVac (Savant Instruments, Holbrook, CA).  RNA samples (6-7 µg/µL) were stored in 100 µL TE buffer at -80°C.

Microarray Studies:  Total RNA obtained from induced chronically infected and corresponding uninfected parental cells were used for microarray experiments.  For each time point, RNA from the induced chronically infected ACH-2 cells and RNA from the corresponding induced, uninfected A3.01 cells were compared to minimize effects due to PMA induction. Microarrays were obtained from the National Cancer Institute Microarray Facility, Advanced Technology Center (Gaithersburg, MD).  The microarrays (Hs. UniGem2) contained 10,368 cDNA spots on each glass slide. The cDNAs were selected for spotting on the slides based on their known or probable involvement in oncogenesis, signal transduction, apoptosis, immune function, inflammatory pathways, cellular transport, transcription, protein translation and other important cellular functions.  A number of expressed sequence tags (ESTs) from unknown genes homologous to known genes and cDNAs encoding housekeeping genes were also included in these gene sets.  For each time point, 50 µg of total RNA from PMA induced ACH-2 cells and 70 µg of total RNA from PMA induced A3.01 cells was labeled with Cy-3-dUTP and Cy-5-dUTP respectively.  Higher amounts of RNA were used for Cy-5 labeling to minimize the disparities in dye incorporation.  Each sample of RNA from PMA-induced, infected cells from a particular time point was compared with RNA from the corresponding PMA-induced, uninfected cells from the same time point for subsequent hybridization to the same array to ensure accurate comparisons and to eliminate inter-array variability. Following reverse transcription, the labeled cDNAs were then combined and purified using MicroCon YM-30 (Millipore, Bedford, MA) spin column filters, to remove any unincorporated nucleotides. 8-10 µg each of Cot-1 DNA, (Boehringer Mannheim, Indianapolis, IN), yeast tRNA (Sigma) and polyA (Amersham Biosciences) were added to the reaction mixture and heated at 100°C for 1 minute.  Hybridization of the labeled cDNA to the microarray was carried out at 65°C overnight, followed by washes with 1X SSC, 0.2X SSC and 0.05X SSC respectively.  The slides were dried by centrifugation at 1000 rpm for 3 minutes and then scanned as described below.

Microarray Scanning and Data Analysis:  The slides were scanned using an Axon GenePix 4000 scanner (Axon Instruments, Union City, CA). The photomultiplier tube values (PMT) were adjusted to obtain equivalent intensities at both wavelengths used, 635 nm and 532 nm for the Cy5 and Cy3 channels respectively.  Image analysis was performed using GenePix analysis software (Axon Instruments) and data analysis was performed using the microArray Database (mAdb) system hosted by the Center for Information Technology and Center for Cancer Research at NIH (http://nciarray.nci.nih.gov/).
Keywords = HIV
Keywords = latency
Keywords: time-course

first: Steven

middle: L

last: Zeichner


title: Host Cell Gene Expression During HIV-1 Latency in Chronically Infected Cell Lines

summary:
Cells: ACH-2, A3.01, J1.1, and U1 cells were obtained through the NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH.  U-937 cells were obtained from American Type Culture Collection (Manassas, VA).  ACH-2, J1.1 and U1 are chronically infected cell lines harboring HIV-1 LAV strain, while A3.01, Jurkat, and U-937 are the corresponding parental uninfected cell lines.  Cells were grown in RPMI-1640 (Invitrogen, San Diego, CA) with 10% fetal bovine serum (FBS, Invitrogen), 5% penicillin-streptomycin (Invitrogen), and 2mM glutamine (Invitrogen).  Cells were maintained at a concentration of 1x10e6 cells/ml in T-175 flasks. Cell concentrations and cell viability were monitored throughout the experiment. Cells were harvested by centrifugation at 1000 rpm for 10 minutes.  Harvested cells were washed thrice with ice-cold PBS to remove media; cell pellets were snap frozen using ethanol-dry ice mixture and stored at -80°C for subsequent RNA extraction.
In order to compare expression profiles of chronically infected cell lines, ACH-2, U1, and J1.1 and their uninfected parental cell lines, A3.01, U-937 and Jurkat cells respectively, were grown under identical conditions but in presence of AZT (250 nM) in growth media and cells were harvested as described above. In these studies, no inducing agent was used in either chronically infected or uninfected parental cell lines so as to study changes in cellular gene expression cells latently infected with HIV and uninfected cells.
Total RNA Extraction:  Total RNA was extracted using RNEasy Midiprep Kits per manufacturer's protocol (Qiagen, Valencia, CA).  RNA concentrations and purity were measured by spectrophotometry, RNA quality (absence of RNA degradation) was assessed by gel electrophoresis.  RNA concentration was adjusted to the levels required for subsequent microarray experiment protocols by concentration in a SpeedVac (Savant Instruments, Holbrook, CA).  RNA samples (6-7 µg/µL) were stored in 100 µL TE buffer at -80°C.

Microarray Studies:  Total RNA obtained from chronically infected and corresponding uninfected parental cells were used for microarray experiments.  For each cell line, RNA from the chronically infected cells (ACH-2, J1.1 or U1)and RNA from the corresponding induced, uninfected cells (A3.01 , Jurkat or U937) were compared on the same array. Microarrays were obtained from the National Cancer Institute Microarray Facility, Advanced Technology Center (Gaithersburg, MD).  The microarrays (Hs. UniGem2) contained 10,368 cDNA spots on each glass slide. The cDNAs were selected for spotting on the slides based on their known or probable involvement in oncogenesis, signal transduction, apoptosis, immune function, inflammatory pathways, cellular transport, transcription, protein translation and other important cellular functions.  A number of expressed sequence tags (ESTs) from unknown genes homologous to known genes and cDNAs encoding housekeeping genes were also included in these gene sets.  For each array, 50 µg of total RNA from chronically infected cells and 70 µg of total RNA from corresponding uninfected cells was labeled with Cy-3-dUTP and Cy-5-dUTP respectively.  Higher amounts of RNA were used for Cy-5 labeling to minimize the disparities in dye incorporation. Following reverse transcription, the labeled cDNAs were then combined and purified using MicroCon YM-30 (Millipore, Bedford, MA) spin column filters, to remove any unincorporated nucleotides. 8-10 µg each of Cot-1 DNA, (Boehringer Mannheim, Indianapolis, IN), yeast tRNA (Sigma) and polyA (Amersham Biosciences) were added to the reaction mixture and heated at 100°C for 1 minute.  Hybridization of the labeled cDNA to the microarray was carried out at 65°C overnight, followed by washes with 1X SSC, 0.2X SSC and 0.05X SSC respectively.  The slides were dried by centrifugation at 1000 rpm for 3 minutes and then scanned as described below.

Microarray Scanning and Data Analysis:  The slides were scanned using an Axon GenePix 4000 scanner (Axon Instruments, Union City, CA). The photomultiplier tube values (PMT) were adjusted to obtain equivalent intensities at both wavelengths used, 635 nm and 532 nm for the Cy5 and Cy3 channels respectively.  Image analysis was performed using GenePix analysis software (Axon Instruments) and data analysis was performed using the microArray Database (mAdb) system hosted by the Center for Information Technology and Center for Cancer Research at NIH (http://nciarray.nci.nih.gov/).
Keywords = HIV
Keywords = Latency
Keywords: other


title: CX43 heterozygous, Cx43 null and Cx32 null vs wildtype neonatal mouse brain

status: Public on Nov 12 2004

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

summary: Cy3-labeled cDNA from brains of neonatal C57BL Cx43 null, Cx43 heterozygous and Cx32 null mice were compared among themselves and to Cy3-labeled cDNA from brains of neonatal C57BL wildtype mice through Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.

first: Sanda

first: Marcia

last: Urban-Maldonado

first: David

last: Spray


title: Hac1p control of unfolded protein response

status: Public on Aug 18 2004

city: Chicago

first: Jess

last: Leber

address: 920 E. 58th Street CLSC 615

department: Microbiology

institute: The University of Chicago

summary:
All samples are of the genotype listed in the title (e.g. W303, delta-hac1, etc.).  Samples treated with DTT were treated for 60 min with 6 mM DTT.  Samples  with 'dT' in the title were concurrently shifted from 23°C to 37°C; otherwise, samples were grown at 30°C.  All array data is from two independent experiments, with data listed as two files designated "A" and "B" , except for the "ADH1pro DTT" expt, which was performed once.  The data sets were filtered with NOMAD to include only "high quality" data.
Keywords: other

middle: H

first: Sebastian

last: Bernales

first: Peter

last: Walter


title: CEA_SGF:E00005#LIF

status: Public on Jul 01 2004

city: Villejuif

first: Dalila

last: Sekkai

department: hematopoiesis and stem cell

institute: IGR

summary:
In order to identify the genes involved in LIF/gp130 self-renewal response, we analyzed the transcriptome of Gs2 ES cells induced to differentiate upon LIF withdrawal for 16h, 24h and 48h (LIF16, LIF24 and LIF48 respectively)and compared them to that of undifferentiated ES Gs2 cells continuously maintained in the presence of LIF.
Since this cell line also carry a tetracycline regulatable dominant negative form of Stat3 (Stat3F, all the experiment was done in the presence of Tetracycline (tet ON) to avoid Stat3F expression.
Keywords: time-course


title: CEA_SGF:E00004#TetOFF_Stat3F

summary:
The goal of this study was to identify the target genes of Stat3 involved in murine ES cell self-renewal. To achieve this goal, we used the Gs2 ES cell line expressing an inducible dominant negative mutant of Stat3 (Stat3F) in wich Y705 is mutated to phenilalanine. The Gs2 ES cells are routinely maintained in the presence of LIF 1000 U/ml and tetracycline 1µg/ml (LIF/ON). In this condition, Stat3F is not expressed and the cells are maintained in an undifferentiated phenotype. Upon tetracycline removal but inthe presence of LIF (Tet OFF condition) Stat3F is expressed and the cells differentiate despite the presence of LIF. We thus performed microarray analysis of the transcriptome of ES cells after 16h, 24h and 48h after Tetracycline removal (OFF16; OFF24 and OFF48) respectively)and compared them to Gs2 ES cells maintained in the continuous presence of LIF and tetracyclin (LIF/ON).
Keywords: time-course


title: Cellular interaction with S. aureus bacteria or with bacterial supernatant

status: Public on Jun 03 2004

city: Sophia Antipolis

first: Chimene

last: Moreilhon

institute: CNRS

summary:
Each condition (cellular interaction with bacteria or with bacterial supernatant) was hybridized on 6 slides (3 slides, corresponding to different interactions and RNA extractions, were swapped).

Keywords: parallel sample


title: TIAR represses c-Myc biosynthesis following ultraviolet light irradiation-2

status: Public on Jun 02 2004

first: Myriam

last: Gorospe

address: 5600 Nathan Shock Drive

institute: NIA

summary:
Untreated or 20 J/m2 UVC treated RKO cells were collected and RNA from either whole-cell lysates or from polysomal fractions was extracted at 0 (untreated), 3, 6, and 12 h after treatment.  RNA from whole-cell lysates or each of 11 polysomal fraction was reverse-transcribed in the presence of [α-33P]dCTP and the radiolabeled product used to hybridize human cDNA arrays.  The experiment was repeated using three independent sample sets.  The samples were named T-c-A, T-c-B, T-c-C, T-3h-A, T-3h-B, T-3h-C, T-6h-A, T-6h-B, T-6h-C, T-12h-A, T-12h-B, T-12h-C, P-c-1-A, P-c-2-A, P-c-3-A, P-c-4-A, P-c-5-A, P-c-6-A, P-c-7-A, P-c-8-A, P-c-9-A, P-c-10-A, P-c-11-A, P-c-1-B, P-c-2-B, P-c-3-B, P-c-4-B, P-c-5-B, P-c-6-B, P-c-7-B, P-c-8-B, P-c-9-B, P-c-10-B, P-c-11-B, P-c-2-C, P-c-3-C, P-c-4-C, P-c-5-C, P-c-6-C, P-c-7-C, P-c-8-C, P-c-9-C, P-c-10-C, P-c-11-C, P-3h-1-A, P-3h-2-A, P-3h-3-A, P-3h-4-A, P-3h-5-A, P-3h-6-A, P-3h-7-A, P-3h-8-A, P-3h-9-A, P-3h-10-A, P-3h-11-A, P-3h-1-B, P-3h-2-B, P-3h-3-B, P-3h-4-B, P-3h-5-B, P-3h-6-B, P-3h-7-B, P-3h-8-B, P-3h-9-B, P-3h-10-B, P-3h-11-B, P-3h-1-C, P-3h-2-C, P-3h-3-C, P-3h-4-C, P-3h-6-C, P-3h-7-C, P-3h-8-C, P-3h-9-C, P-3h-10-C, P-3h-11-C, P-6h-1-A, P-6h-2-A, P-6h-3-A, P-6h-4-A, P-6h-5-A, P-6h-6-A, P-6h-7-A, P-6h-8-A, P-6h-9-A, P-6h-10-A, P-6h-11-A, P-6h-1-B, P-6h-2-B, P-6h-3-B, P-6h-4-B, P-6h-5-B, P-6h-6-B, P-6h-7-B, P-6h-8-B, P-6h-9-B, P-6h-10-B, P-6h-11-B, P-6h-1-C, P-6h-2-C, P-6h-3-C, P-6h-4-C, P-6h-5-C, P-6h-6-C, P-6h-7-C, P-6h-8-C, P-6h-9-C, P-6h-10-C, P-6h-11-C, P-12h-1-A, P-12h-2-A, P-12h-3-A, P-12h-4-A, P-12h-5-A, P-12h-6-A, P-12h-7-A, P-12h-8-A, P-12h-9-A, P-12h-10-A, P-12h-11-A, P-12h-1-B, P-12h-2-B, P-12h-3-B, P-12h-4-B, P-12h-5-B, P-12h-6-B, P-12h-7-B, P-12h-8-B, P-12h-9-B, P-12h-10-B, P-12h-11-B, P-12h-1-C, P-12h-2-C, P-12h-3-C, P-12h-6-C, P-12h-7-C, P-12h-8-C, P-12h-9-C, P-12h-10-C, P-12h-11-C.  ‘T’ represents total RNA, ‘P’ represents RNA from polysomes fractions, ‘c’ represents RNA from untreated cells, ‘3h’ represents RNA from cells collected 3 h after UVC treatment, ‘6h’ represents RNA from cells collected 6 h after UVC treatment, ‘12h’ represents RNA from cells collected 12 h after UVC treatment.  The numbers 1-11 correspond to the each polysomal fraction.  The letters A, B and C correspond to the three independent experimental datasets.
Keywords = post-transcriptional / translation / nascent protein synthesis / stress response / ribonomics
Keywords: ordered

first: Krystyna

last: Mazan-Mamczarz

first: Ashish

last: Lal

first: Jennifer

last: Martindale

first: Tomoko

last: Kawai


title: TIAR represses c-Myc biosynthesis following ultraviolet light irradiation

status: Public on May 27 2004

summary:
RNA was isolated from material that had been subjected to immunoprecipitation (IP) from RKO cells that were either left untreated or irradiated with 20 J/m2 UVC and collected 1h later; IP assays were carried out using either an antibody recognizing RNA-binding protein TIAR, or using a control IgG1 antibody.  RNA was reverse-transcribed in the presence of [alpha-33P]dCTP and the radiolabeled product used to hybridize human cDNA arrays.  The experiment was repeated using three independent sample sets. The samples were numbered Tc-1, Tc-2, Tc-3, Tuv-1, Tuv-2, Tuv-3, IgG1c-1, IgG1c-2, IgG1c-3, IgG1uv-1, IgG1uv-2, and IgG1uv-3. ‘Tc’ denotes RNA from IP reactions using untreated cells and anti-TIAR antibody, ‘Tuv’ denotes RNA from IP reactions using UVC-treated cells and anti-TIAR antibody, ‘IgG1c’ denotes RNA from IP reactions using untreated cells and anti-IgG1 antibody, and ‘IgG1uv’ denotes RNA from IP reactions using UVC-treated cells and anti-IgG1 antibody.  The numbers 1, 2 and 3 correspond to the three independent experimental datasets.
Keywords = post-transcriptional / translation / nascent protein synthesis / stress response / ribonomics
Keywords: ordered


title: Concurrent Versus Individual Binding of HuR and AUF1 to Common Labile Target mRNAs

status: Public on May 04 2004

summary:
RNA was isolated from material that had been immunoprecipitated (IP) from Hela cells using antibodies recognizing RNA-binding proteins HuR or AUF1, as well as using a control IgG1 antibody. RNA was reverse-transcribed in the presence of [alpha-33P]dCTP and the radiolabeled product used to hybridize human cDNA arrays. The experiment was repeated using three independent sample sets. The samples were numbered HuR-1, HuR-2, HuR-3, AUF1-1, AUF1-2, AUF1-3, IgG1-1, IgG1-2, IgG1-3. HuR represents RNA from IP reactions using an anti-HuR antibody, AUF1 represents RNA from IP reactions using an anti-AUF1 antibody and, IgG1 represents RNA from IP reactions using an anti-IgG1 antibody. The numbers 1, 2 and 3 correspond to the three independent experimental datasets.
Keywords = RNa-binding protein
Keywords = mRNA stability
Keywords = exosome
Keywords = polysome
Keywords = RNA motif
Keywords: ordered

first: Xiaoling

last: Yang


title: Rosetta_Merck_CEPH_Study

status: Public on Sep 04 2004

city: Denver

first: Stephanie

last: Santorico

state: CO

department: Mathematical and Statistical Sciences

institute: University of Colorado Denver

summary:
Array data for "Genetic Inheritance of Gene Expression in Human Cell Lines"
Monks, et al., American Journal of Human Genetics (2004)
Keywords = Genetics of Gene Expression
Keywords = human
Keywords = CEPH family
Keywords: repeat sample

last: Monks

first: Amy

last: Leonardson

first: Haoyuan

last: Zhu

first: Paige

last: Cundiff

first: Paul

last: Pietrusiak

first: Stephen

middle: W

last: Edwards

first: John

last: Phillips

first: Alan

last: Sachs

first: Eric

middle: E

last: Schadt


title: Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation

status: Public on Aug 04 2004

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

summary:
Delayed implantation occurs in many mammals, but the underlying mechanisms that direct this process remain largely unknown. In mice, ovariectomy prior to the preimplantation ovarian estrogen secretion on day 4 of pregnancy initiates blastocyst dormancy, which can be maintained for more than 200 days by continued progesterone
Keywords: other

first: Toshio

last: Hamatani

first: Takiko

last: Daikoku

first: Haibin

last: Wang

first: Hiromichi

last: Matsumoto

first: Carter

last: Mo

first: Sudhansu

last: Dey


title: HPP4_cDNA

status: Public on Feb 12 2004

first: Ellen

last: Sterrenburg

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

summary:
Time series experiment on healthy human primary skeletal muscle cells (HPP4)
Keywords: time-course


title: A404 Smooth Muscle Cell Differentiation

status: Public on Jun 30 2004

city: Stanford

first: Joshua

middle: M.

last: Spin

address: 300 Pasteur Drive

institute: Stanford University

summary:
In vitro time course experiment using the A404 clone of P19 mouse embryonal carcinoma cells to evaluate SMC differentiation in response to retinoic acid followed by phenotype-specific selection with puromycin. Four time points of 5-6 biological replicates each were performed.
Keywords: time-course

first: J

middle: M

first: S

last: Nallamshetty

first: R

last: Tabibiazar

first: E

last: Ashley

middle: Y

last: King

first: M

last: Chen

first: P

last: Tsao

first: T

last: Quertermous


title: Skeletal muscle cell fusion time course

summary:
Time course experiment of healthy primary skeletal muscle cells KM109, KM108 and HPP4 after initiation of fusion

This SuperSeries is composed of the SubSeries listed below.


title: T lymphocyte activation gene identification by coregulated expression on DNA microarrays

status: Public on Feb 01 2004

city: Kirkland

first: Mao

last: Mao

department: Biology

institute: Rosetta Inpharmatics

summary:
High-capacity methods for assessing gene function have become increasingly important because of the increasing number of newly identified genes emerging from large-scale genome sequencing and cDNA cloning efforts. We investigated the use of DNA microarrays to identify uncharacterized genes specifically involved in human T cell activation. Activation of human peripheral blood T lymphocytes induced significant changes in hundreds of transcripts, but most of these were not unique to T cell activation. Variation of experimental parameters and analysis techniques allowed better enrichment for gene expression changes unique to T cell activation. Best results were achieved by identification of genes that were most highly coregulated with the T-cell-specific transcript interleukin 2 (IL2) in a "compendium" of experiments involving both T cells and other cell types. Among the genes most highly coregulated with IL2 were many genes known to function during T cell activation, together with ESTs of unknown function. Four of these ESTs were extended to novel full-length clones encoding T-cell-regulated proteins with predicted functions in GTP metabolism, cell organization, and signal transduction.
Keywords: other

first: Jerald

middle: P

last: Radich

first: Sergey

last: Stepaniants

first: Matt

last: Biery

first: Terry

last: Ward

first: Greg

last: Schimmack

first: Sumire

last: Kobayashi

first: Michael

last: Carleton

first: John

last: Castle

first: Johanna

last: Lampe

first: Julja

last: Burchard

first: Janell

last: Schelter

first: Hongyue

last: Dai

first: Yudong

middle: D

last: He

first: Peter

last: Linsely


title: KM109

first: Ellen

last: Sterrenburg

summary:
Time-course experiment of healthy primary skeletal muscle cells; KM109
Keywords: time-course


status: Public on Apr 03 2004

city: Tokyo

first: Motoyuki

last: Otsuka

department: Department of Gastroenterology

institute: University of Tokyo

summary:
Acyclic retinoid induction of HepG2 cells
Keywords: other


title: CEA_SGF:E00008#transgenic_IIb-tk

status: Public on Apr 09 2004

first: Thierry

last: Kortulewski

address: 2 rue Gaston Cremieux

institute: CEA/DRR/SGF/LGRH

summary:
To investigate genes that are involved in hematopoietic cells production in vivo, we used microarray technology combined with a transgenic mouse model IIb-tk previously developed in our laboratory (Tropel et al., 1997). In these mice, the promoter region of the murine CD41 (GPIIb) gene was used to target the expression of the thymidine kinase (tk) toxigene in cells specifically expressing the CD41 gene. The strength of the model resides in the fact that the depletion of the entire myelo-megakaryocytic lineage including stem cells/early progenitors by ganciclovir (GCV) administration could be inverted by discontinuing the treatment. A nearly full recovery of mature myelo-megakaryocytic cells is then observed within 3 days. To determine at the molecular level how BM cells could be regenerated in vivo following the eradication of all myeloid progenitors by the GCV treatment, microarray technology was applied. The strategy involved monitoring early transcriptional changes for the first 3-day of BM regeneration.
Keywords: time-course


title: KM108_cDNA

summary:
Timecourse experiment of healthy human primary skeletal muscle cells (KM108)
Keywords: time-course


title: Lung cancer

status: Public on Feb 11 2004

city: Koto-ku

first: Yuichi

last: Ishikawa

state: Tokyo

address: 3-8-31 Ariake

institute: Cancer Insitute

summary:
Two prognostically significant subtypes of high-grade lung neuroendocrine tumors independent of small-cell and large-cell neuroendocrine carcinomas identified by gene expression profiles.

BACKGROUND: Classification of high-grade neuroendocrine tumors (HGNT) of the lung currently recognises large-cell neuroendocrine carcinoma (LCNEC) and small-cell lung carcinoma (SCLC) as distinct groups. However, a similarity in histology for these two carcinomas and uncertain clinical course have led to suggestions that a single HGNT classification would be more appropriate. Gene expression profiling, which can reproduce histopathological classification, and often defines new subclasses with prognostic significance, can be used to resolve HGNT classification. METHODS: We used cDNA microarrays with 40386 elements to analyze the gene expression profiles of 38 surgically resected samples of lung neuroendocrine tumors and 11 SCLC cell lines. Samples of large-cell carcinoma, adenocarcinoma, and normal lung were also included to give a total of 105 samples analyzed. The data were subjected to filtering to yield informative genes before unsupervised hierarchical clustering that identified relatedness of tumor samples. FINDINGS: Distinct groups for carcinoids, large-cell carcinoma, adenocarcinoma, and normal lung were readily identified. However, we were unable to distinguish LCNEC from SCLC by gene expression profiling. Three independent rounds of unsupervised hierarchical clustering consistently divided SCLC samples into two main groups with LCNEC samples largely integrated with these groups. Furthermore, patients in one of the groups identified by clustering had a significantly better clinical outcome than the other (83% vs 12% survived for 5 years; p=0.0094. None of the highly proliferative SCLC cell lines subsequently analyzed clustered with this good-prognosis group. INTERPRETATION: Our findings show that HGNT of the lung can be classified into two groups independent of SCLC and LCNEC. To this end, we have identified many genes, some of which encode well-characterized markers of cancer that distinguish the HGNT groups. These results have implications for the diagnosis, classification, and treatment of lung neuroendocrine tumors, and provide important insights into their underlying biology.
Keywords: other

last: Jones

first: Carl

last: Virtanen

first: Daisuke


title: Rosetta_Merck_Splicing_Experiment

status: Public on Dec 19 2003

department: Informatics

institute: Merck

summary:
This series represents 52 tissues hybridized across 5 different chip patterns. Probes were placed at every exon-exon junction in each transcript.
Keywords = junction alternate splicing oligonucleotide
Keywords: parallel sample

first: Jason

last: Johnson

first: Philip

last: Garrett-Engele

first: Patrick

last: Loerch

first: Zhengyan

last: Kan

first: Christopher

last: Armour

first: Ralph

last: Santos

first: Eric

last: Schadt

first: Roland

last: Stoughton

first: Daniel

last: Shoemaker