title: C. elegans daf2 mutant adults

status: Public on Sep 14 2004

city: London

first: Joshua

middle: J.

last: McElwee

address: Gower Street

department: Biology

institute: University College London

summary:
Analysis of gene expression in long-lived daf-2 mutants for the insulin/IGF-1 receptor. daf-2(e1370) and daf-2(m577) alleles each examined as single and as double mutations with the daf-16(df50) allele. DAF-2 regulates DAF-16, a transcription factor. Results provide insight into longevity.
Keywords: other

first: Eugene

last: Schuster

first: Eric

last: Blanc

first: James

middle: H

last: Thomas

first: David

last: Gems


title: Rpd3 and histone H3 and H4 deletions/mutations

status: Public on Sep 04 2004

city: Albany

first: Randall

middle: Heywood

last: Morse

state: NY

country: USA

institute: Wadsworth Center

summary:
Signal intensity data for rpd3 delete, H3delta(1-28), H3(K4,9,14,18,23,27Q), H4delta(2-26), H4(K5,8,12,16Q), rpd3 delete H3delta(1-28), and rpd3 delete H4(K5,8,12,16Q) yeast grown in rich (YPD) media
Keywords = histones
Keywords = chromatin
Keywords = rpd3
Keywords = HDAC
Keywords = histone deacetylase
Keywords = yeast
Keywords: other

first: Nevin

last: Sabet

first: Sam

last: Volo

first: Cailin

last: Yu

middle: P

last: Madigan


title: PKR overexpression

status: Public on Sep 22 2004

city: Montreal

first: Rob

last: Sladek

state: PQ

address: 740 avenue du Docteur Penfield

country: Canada

institute: Montreal Genome Centre

summary:
Global analysis of gene expression in NIH3T3 cells over-expressing RNA-dependent serine/threonine protein kinase (PKR).
Keywords: other

first: Olivier

last: Donzé

first: Jing

last: Deng

first: Joseph

last: Curran

first: Robert

first: Didier

last: Picard

first: Nahum

last: Sonenberg


title: CD14+ cell analysis

status: Public on Sep 15 2004

city: Seattle

first: Lynn

last: Graf

state: WA

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary:
Comparison of gene expression in CD14 cells from peripheral blood and G-CSF-mobilized peripheral blood to investigate why the latter may be beneficial for allogeneic transplant recipients.
Samples from 2-3 donors were pooled for each sample. All cells were freshly isolated after ficoll separation of mononuclear cells.
Keywords = CD14, monocyte, PBMC, GPBMC, peripheral blood
Keywords: other

first: Beverly

last: Torok-Storb


title: Natural variation in human gene expression

status: Public on Aug 12 2004

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary:
We measured the baseline expression levels of genes in members of the CEPH pedigrees using Affymetrix Human Genome Focus Arrays.  Arrays were analyzed using MAS 5.0 software (Affymetrix).
Keywords = natural variation
Keywords = human
Keywords: other

first: Cliona

middle: M

last: Molony

first: Teresa

last: Weber

middle: L

last: Devlin

first: Kathryn

middle: G

last: Ewens

first: Richard

middle: S

last: Spielman

first: Vivian

last: Cheung


title: DC differentiation from DC progenitor in vitro

status: Public on Sep 30 2004

city: Aachen

first: Thomas

last: Hieronymus

address: Pauwelsstr. 30

department: Institute for Biomedical Engineering - Cell Biology

country: Germany

institute: University Medical School, RWTH Aachen

summary:
FLT3+CD11b+ DC progenitor was amplified in vitro from mouse bone marrow. DC were differentiated using GM-CSF and analyzed at day 7 and day 10 of differentiation and after 16h TNFalpha stimulation at day 10
Keywords: time-course


title: Naive and  memory B6.2.16 CD8 T cell(11K  A and B)

status: Public on Aug 05 2004

city: Chicago

first: Philip

middle: George

last: Ashton-Rickardt

state: IL

address: 924 E.57th Street

department: Pathology

institute: The University of Chicago

summary:
Naive B6.2.16 CD8 T cells (>85% pure) were isolated from the lymph nodes (LN) of female RAG1-deficient B6.2.16 mice.  B6.2.16 CD8 T cell effectors were generated by culturing splenocytes from female RAG1-deficient B6.2.16 mice with HY peptide for 4 d and adoptively transferred into female RAG1-deficient mice.  After 200 d, memory B6.2.16 CD8 T cells (>80% pure) were recovered from the spleens and LNs by magnetic bead sorting. Sample proRNA from naïve and memoryB6.2.16 CD8 T cells was isolated using Trizol(r) Reagent and used to make cRNA for hybridization according to Affymetrix protocols.
Keywords: other

first: Ni

last: Liu

first: Tiphanie

last: Phillips

first: Manling

last: Zhang

first: Yue

last: Wang

last: Opferman

first: Ramila

last: Shah


title: Comparison of Drosophila melanogaster Malpighian tubule v whole fly

status: Public on Aug 24 2004

city: Glasgow

first: Julian

last: Dow

address: Anderso College Complex

department: Molecular and Integrative Physiology

country: United Kingdom

institute: University of Glasgow

summary:
This is an affymetrix array experiment comparing the transcriptome of the Malpighian tubule (or renal tubule) of 7-day adult Oregon R strain Drosophila melanogaster with matched whole fly samples.
There are five tubule samples (each derived from approx 1000 tubules (!)), and 5 matched whole-fly samples. i.e. tubule 2 is dissected from the same vial as WholeFly2.
As the tubule is probably the premier tissue for true physiology in Drosophila, the dataset can usefully be interrogated in conjunction with the detailed physiological understanding of the tissue: see
http://fly.to/tubules

first: Jing

first: Laura

last: Kean

first: Jingli

last: Yang

first: Adrian

middle: K

last: Allan

first: Shireen

middle: A

last: Davies

first: Pawel

last: Herzyk


title: Distribution of different proteins related to sister chromatid cohesion during the cell cycle.

status: Public on Jun 29 2004

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

summary:
This series is a supplementary data set for the manuscript titled  "Cohesin relocation from sites of chromosomal loading to places of convergent transcription"
All data shown in the paper were registered (30 ChIP-chip and one transcription data).

Experimental design:
1.	Type of experiment:
a.	ChIP (Chromatin immunoprecipitation) analysis hybridised to a high density oligonucleotide array. The S. cerevisiae chromosome VI array described by Katou et al. (2003) Nature 424, 1078-83 has been used. Newly developed S. cerevisiae chromosomes III-V and S. pombe chromosomes 2-3 oligonucleotide arrays produced by Affymetrix have also been used.
b.	Gene expression profile analysis of S. cerevisiae.

2.	Experimental factors:
a.	Distribution of different proteins related to sister chromatid cohesion or condensation during the cell cycle, mainly in G1 (alpha-factor arrested cells), S-phase (HU arrested cells) and metaphase (Nocodazole arrested cells).
b.	Gene expression profile analysis of logarithmically growing cells.

3.	Number of hybridizations performed:
a.	ChIP analysis: 32
b.	Gene expression: 1

4.	Hybridisation design:
ChIP analysis: comparison of ChIP fraction with SUP (supernatant) fraction

5.	Quality control: Duplication, confirmation using different tags, different subunits of the same complex, and different yeast strain backgrounds (W303, BY4741, and SK1). Checking of the ChIP fraction by Western blotting. Checking amount of mRNA by RT-PCR.

6.	URL of supplemental website:
GEO Accession number: GSE1461

Web site: http://chromosomedynamics.bio.titech.ac.jp

Samples used, extract preparation and labeling:

1.	Origin of the biological sample
Budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe)

2.	Manipulation of the samples and the protocols used:
a.	Mitotic budding yeast cells were synchronised in G1 with alpha-factor (2uM) and then released at 23ºC into medium containing 200 mM HU or 7.5 ug/ml Nocodazole for 60 min and 150 min, respectively. scc2-4 cells were shifted to 37ºC 60 min before alpha-factor release. Heat-shock treatment has been done at 37ºC for 15 minutes.
b.	Meiotic budding yeast cells were collected 4 hours after meiosis induction at 23ºC.
c.	Mitotic fission yeast cells were grown logarithmically in minimum medium (MM).

Cells were fixed over night in 1% formaldehyde at 4ºC.

3.	Protocols for preparing extracts:
a.	ChIP analysis: Extract preparation was processed following the Shirahige lab protocol (http://chromosomedynamics.bio.titech.ac.jp ). 5x10^8 cells were disrupted using Multi-Beads Shocker (MB400U, YASUI KIKAI, Osaka). Whole cell extract was sonicated to obtain 400-600 bp genomic DNA fragments. Anti-HA monoclonal antibody (clone 16B12, CRP Inc., Denver, PA) and anti-Flag monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) coupled to Dynabeads (Dynal, protein A Dynabeads) were used for chromatin immunoprecipitation. The immunprecipates were eluted and incubated over night at 65ºC to reverse the cross-link. Immunoprecipitated genomic DNA was incubated with proteinase K, extracted 2 times with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RnaseA. The DNA was then purified using the Qiagen PCR purification kit, and concentrated by ethanol precipitation. The DNA was amplified by PCR after random priming. 10 ug of amplified DNA was digested with Dnase I to a mean size of 100 bp. After Dnase I inactivation at 95ºC, fragments were labelled as detailled below.
b.	Gene expression analysis: Total RNA was prepared using FastRNA Pro Red Kit (BIO 101 Systems) according to the manufacturer’s instructions. 10 ug of total RNA was reverse transcribed according to the protocol recommended by Affymetrix. In vitro transcription was performed on 1 ug of cDNA. cRNA was cleaned and fragmented by heating. 20 ug of fragmented cRNA were hybridised.

4.	Labelling protocol
DNA fragments were end-labelled by addition of 25 U of Terminal Transferase and 1 nmol Biotin-N6ddATP (NEN) for 1 hour at 37ºC as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). The entire sample was used for hybridization.

Hybridization procedures and parameters:
Hybridization, blocking and washing were carried out as previously described (http://chromosomedynamics.bio.titech.ac.jp). Each sample was hybridized to the array in 150 ul containing 6xSSPE; 0.005% TritonX-100; 15 ug fragmented denatured salmon sperm DNA (Gibco-BRL); 1 nmole 3’biotin labelled control oligonucleotide (oligo B2, Affymetrix). Samples were denatured at 100ºC for 10 minutes, and then put on ice before being hybridized for 16 hours at 42ºC in an hybridization oven (GeneChip Hybri. Oven 320, Affymetrix). Washing and scanning protocol (FlexMidi-euk2v3-450) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix).

Measurement data and specifications:
S. cerevisiae arrays were scanned using the HP GeneArray Scanner (Affymetrix) at an emission wavelength of 560 nm, resolution 7.5 uM. S. pombe arrays were scanned by GeneChip Scanner 3000 (Affymetrix) at an emission wavelength of 570 nm, resolution 2.5 uM. Grids were aligned to scans following the library array description. Primary data analyses were carried out using Affymetrix Microarray Suite Ver.5.0 software to obtain signal intensity, fold change value, change p-value and detection p-value. The detailed information of this analysis is available at http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf and http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf
To discriminate significant signals for binding to DNA (dark grey signals), signals from the ChIP fraction scan were compared to the SUP (supernatant) fraction scan using the 3 following criteria: first, the signal reliability was judged by the detection p-value of each locus (p-value ≤0.025); secondly, reliability of binding ratio was judged by change p-value (p-value ≤0.025); thirdly, only clusters of at least 3 contiguous loci responding to the 2 previous criteria were selected as significantly enriched locus. The light grey signals represent the statistically not significantly enriched signals. The software to present the result (chr6viewer) is available at http://everythingchromovi.gsc.riken.go.jp. The raw and transformed data files are available at GEO database website and at our web site http://chromosomedynamics.bio.titech.ac.jp.

Array Design
1.	General array design: in situ synthesized arrays by Affymetrix
2.	Availability of arrays: commercially available from Affymetrix
3.	Location and ID of each spot on arrays: available at our web site (http://chromosomedynamics.bio.titech.ac.jp) and from Affymetrix on request
4.	Probe type: oligonucleotide
5.	The arrays used in this study can be purchased from Affymetrix:
Chromosome VI S.cerevisiae: rikDACF, P/N# 510636
Chromosome III,IV,V S.cerevisiae: SC3456a520015F, P/N# 520015
Chromosome II,III S.pombe: S_pombea520106F, P/N# 520106
YGS98 GeneChipsT oligonucleotide arrays: P/N# 900256

Keywords = Yeast Cohesin Condensin Loading Distribution
Keywords: other

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

first: Armelle

last: Lengronne

first: Yuki

last: Katou

first: Saori

last: Mori

first: Shihori

last: Yokobayashi

first: Gavin

last: Kelly

first: Takehiko

last: Itoh

first: Yoshinori

last: Watanabe

first: Frank

last: Uhlmann


title: Two-dimensional transcriptome analysis in chemostat cultures of S. cerevisiae

status: Public on Sep 03 2004

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary:
The goal of this study was to study this interaction by analyzing genome-wide transcriptional responses to four different nutrient-limitation regimes under aerobic and anaerobic conditions in chemostat cultures of S. cerevisiae. This ‘two-dimensional’ approach resulted in a new, robust set of ‘anaerobic’ and ‘aerobic’ signature transcripts for S. cerevisiae, as well as to a refinement of previous reports on nutrient-responsive genes. Moreover, the identification of genes regulated both by nutrient and oxygen availability provided new insight in cross-regulated network and hierarchy in the control of gene expression.
Keywords = S. cerevisiae
Keywords = oxygen availability
Keywords = anaerobiosis
Keywords = chemostat
Keywords = transcriptome
Keywords = nutrient limitation
Keywords = carbon
Keywords = nitrogen
Keywords = sulfur
Keywords = phosphorus.
Keywords: other

first: Siew-Leng

last: Tai

first: Viktor

last: Boer

first: Pascale

first: Michael

middle: C

last: Walsh

first: Johannes

last: de Winde

first: Jack

middle: T

last: Pronk


title: Emphysema Lung Tissue Gene Expression Profiling

status: Public on Jun 01 2004

city: Aurora

first: Christopher

middle: D

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

summary:
Gene expression profiling of lung tissue from undiseased (NML), 'usual' emphysema (EML), and Alpha-1 Antitrypsin Deficiency-related emphysema (ADL).
Keywords = Emphysema
Keywords = COPD
Keywords = Alpha-1 Antitrypsin Deficiency
Keywords: ordered

first: Heiko

last: Golpon

first: Martin

middle: R

last: Zamora

first: Gregory

last: Cosgrove

first: Mark

last: Moore

first: Rubin

last: Tuder

middle: W

last: Geraci

first: Norbert

middle: F

last: Voelkel


title: Extraocular and hindlimb muscle, comparison of wild type and mdx mice, 56 days (Porter lab)

status: Public on Jun 15 2004

city: Cleveland

first: Henry

middle: J.

last: Kaminski

state: OH

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

summary:
Determination of gene expression changes in extraocular and hindlimb (gastrocnemius/soleus) of mdx (dystrophin-deficient) mice at postnatal day 56.  5 independent replicates/muscle group/strain.
Keywords: parallel sample

first: John

last: Porter


title: CCFAlmasan_CaP1

middle: Gilmary

last: Hissong

address: 9500 Euclid Ave.

department: Cancer Biology

institute: Lerner Research Institute Cleveland Clinic Foundation

summary:
The experiment design was multifold, consisting of a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 mixed gamma and beta source, with two additional samples, one exposed to radiation in four fractions instead of all at once, and one containing the parent LNCaP cell line.  PolyA+ RNA was extracted, processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HGU-95 (Av1-E) chip sets, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray
Keywords: ordered

first: Jeffrey

last: Buchsbaum

first: Bendi

last: Gong

first: Subrata

last: Ray

first: Eric

last: Klein

first: Warren

middle: E

last: Heston

first: Alexandru

last: Almasan


title: Drosophila Embryo Culture Gad1 Expressin Neurons

status: Public on Jul 04 2004

city: Duarte

first: Paul

middle: M.

last: Salvaterra

state: CA

address: 1500 E. Duarte Rd.

department: Stem Cell and Developmental Biology

institute: Beckman Research Institute of the City of Hope

summary:
Positively sorted Drosophila Embryo Culture Gad1 (glutamic acid decarboxylase 1) expressing neurons.  FACS sorted after 3-5 days in culture.  Labeled with 2.1 kb Gad1-RFP reporter gene.
Keywords = Gad1 Gad Expressing Neurons Motor
Keywords: other


title: Negative FACS sorted EC neurons

summary:
Drosophila Embryo Cell Culture samples allowed to differentiate 3-5 days in culture.  Samples express a GFP reporter in cholinergic neurons (7.4 kb ChaGal4:UAS-GFP) or an RFP reporter (2.1 kb Gad1-RFP) in glutamic acid decarboxylase 1 expressing Neurons.  This  group of samples contains the negatively sorted FACS fractions (2 Cha and 2 Gad negative samples).
Keywords: other

middle: M


title: Drosophila Cholinergic Neurons

summary:
Neuronal Gene Expression
We are interested in genes that determine the neuronal cellular fate and specific neurotransmitter phenotypes of cells in the nervous system. The reasons for our interest are two fold. First, identification of the genetic pathways operating in specific types of neurons could explain why they die in neurodegenerative diseases such as Alzheimer’s, Parkinson’s and amyotrophic lateral sclerosis. All of these disorders have in common the property that only certain types of neurotransmitter specific neurons degenerate. Secondly, neuronal cell replacement therapies using differentiated stem cell progeny hold the potential to reverse the devastating consequences of neurodegenerative diseases. The genetic personality of specific kinds of neurons must first be defined in order to use proper cells for neuronal replacement and this information will be essential in directing stem cell differentiation into proper developmental pathways.

Our current approach to the problems of specification and neurotransmitter phenotype is to create transgenic animals where different neurotransmitter phenotypes are labeled with a fluorescent reporter gene. Labeled neurons are then isolated using Fluorescence Activated Cell Sorting. The purified populations of neurons are analyzed for their whole genome expression patterns using DNA microarray technology. We have successfully applied this approach using Drosophila cholinergic neurons and are now extending our observations to other classes of neurons that use GABA or glutamate as neurotransmitters. Cholinergic neurons express unique sets of ion channels, receptors and other types of genes. We also see unique sets of transcriptional regulatory proteins, and these may be important in the developmental pathways that result in the production of cholinergic neurons.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Drosophila Embryo Culture Cholinergic Neurons

summary:
FACS sorted Drosophila Embryo Cultured Neurons allowed to differentiate 3-5 days in culture.  Positively sorted samples
Keywords = Cholinergic Neurons
Keywords: other


title: Expression profile of genes in normal and Down syndrome mouse brains MGU74B

status: Public on Jun 06 2004

city: Wako-shi

first: Kazuhiro

last: Yamakawa

state: Saitama

address: 2-1 Hirosawa

institute: RIKEN Brain Science Institute

summary:
Analyses of six Ts1Cje (Down syndrome) and six normal littermate (2N) mouse brains at postnatal day 0.
Keywords: repeat sample


title: Antisense IL-10 treatment in Malignant Murine B-1 Cells

status: Public on May 04 2004

city: Newark

first: Brian

last: McCarthy

state: NJ

address: 185 South Orange Ave

institute: NJ Medical School/UMDNJ

summary:
The New Zealand Black (NZB) mouse is a leukemic model. A cell line, LNC, was derived from malignant cells in the lymph node of a 1 year old NZB. We treated LNC in vitro with 20uM IL-10 antisense, untreated control or scrambled sense and RNA was collected at 24 hours.
Keywords = Interleukin 10
Keywords = IL-10
Keywords = Antisense
Keywords = Malignant
Keywords = B-1 Cell
Keywords: parallel sample

first: Siew

middle: Y

last: Chong

first: George

last: Parker

first: Monique

last: Meramo

first: Ming

last: Zhang

first: Jennifer

last: Czarneski

first: Amal

last: Mansour

first: Yi

last: Lin

first: Elizabeth

last: Raveche


title: Differential gene expression in S284Y flies

status: Public on May 25 2004

city: Kansas City

first: Marco

last: Blanchette

state: MO

institute: Stowers Institute for Medical Research

summary:
RNA were extracted from 5 adult male and 5 adult female dU2AF50 wt and mutant flies grown at either the permisive (25C) or restrictive (30C) temperature for 4 days.
Keywords: other

first: Emmanuel

last: Labourier

first: Donald

last: Rio


title: Nucleo-cytoplasmic mRNA distribution

status: Public on May 01 2004

summary:
Nuclear and cytoplasmic RNA were extracted by hypotonic cell lysis from D.-mel2 cell knock down by RNAi against dU2AF50 or with non-specific dsRNA.
Keywords: other


title: Estrogen-regulated gene expression in human osteosarcoma cells stably transfected with estrogen receptor alpha or beta

status: Public on Apr 10 2004

city: Urbana

first: Fabio

last: Stossi

address: 285 Burrill Hall, 407 S Goodwin

institute: University of Illinois at Urbana-Champaign

summary:
Estrogens exert many important effects in bone, a tissue that contains both estrogen receptors alpha and beta (ERalpha and ERbeta). To compare the actions of these receptors, we generated U2OS human osteosarcoma cells stably expressing ERalpha or ERbeta, at levels comparable to those in osteoblasts, and we characterized their response to estradiol (E2) over time using Affymetrix GeneChip microarrays to determine the expression of approximately 12,000 genes, followed by quantitative PCR verification of the regulation of selected genes. Of the ca. 100 regulated genes we identified, some were stimulated by E2 equally through ERalpha and ERbeta, whereas others were selectively stimulated via ERalpha or ERbeta. The E2-regulated genes showed three distinct temporal patterns of expression over the 48 h time course studied. Of the functional categories of the E2-regulated genes, most numerous were those encoding cytokines and factors associated with immune response, signal transduction, and cell migration and cytoskeleton regulation, indicating that E2 can exert effects on multiple pathways in these osteoblast-like cell lines. Of note, E2 up-regulated several genes associated with cell motility selectively via ERbeta, in keeping with the selective E2 enhancement of the motility of ERbeta-containing cells. On genes regulated equally by E2 via ERalpha or ERbeta, the phytoestrogen genistein preferentially stimulated gene expression via ERbeta. These studies indicate both common as well as distinct target genes for these two ERs, and identify many novel genes not previously known to be under estrogen regulation.
Keywords: other

first: Daniel

middle: H

last: Barnett

first: Jonna

last: Frasor

first: Benita

last: Katzenellenbogen


title: Imatinib effects on CD34+ cells

status: Public on May 24 2004

city: Heidelberg

first: Benedikt

last: Brors

address: INF 280

department: Theor. Bioinformatics

institute: German Cancer Research Center (DKFZ)

summary:
purified CD34+ cells from bone marrow of imatinib-treated patients were compared to those of healthy donors
Keywords = CML
Keywords = CD34+ cells
Keywords = imatinib
Keywords: ordered

first: Frank

last: Neumann

first: Slawomir

last: Kliszewski

first: Ralf

last: Kronenwett


title: E2 and SERM Treatment of MCF-7 Breast Cancer Cells

institute: University of Illinois

summary:
MCF-7 breast cancer cells were treated with E2, ICI 182,789 (ICI), Raloxifene (Ral), and/or trans-hydroxytamoxifen (TOT) for 8 or 48 h.  Duplicate samples are labeled set A or set B.
Keywords: other

middle: S


title: Hypoxia and Hypoxia mimics

status: Public on Feb 27 2004

city: East Lansing

first: John

last: LaPres

state: MI

address: Wilson Avenue

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary:
Comparison between hypoxia (1%O2) and cobalt chloride (100 uM) and deferoxamine (100 uM) and Nickel Chloride (100 uM) in Hep3B cells (human hepatocellular carcinoma cells)
Keywords = Hep3B
Keywords = hypoxia
Keywords = cobalt
Keywords = deferoxamine
Keywords = Nickel
Keywords: ordered

first: Ajith

last: Vengellur

middle: B

last: Hogenesch

middle: J


title: Gene Expression-Based High Throughput Screening: HL-60 Cells Treated with ATRA and PMA

status: Public on Jan 30 2004

city: Cambridge

first: Ken

last: Ross

state: MA

address: 7 Cambridge Center

department: Cancer Genomics

institute: Broad Institute

summary:
We developed a general approach to small molecule library screening called GE-HTS (Gene Expression-Based High Throughput Screening) in which a gene expression signature is used as a surrogate for cellular states and applied it to the identification of compounds inducing the differentiation of acute myeloid leukemia cells. In screening 1,739 compounds, we identified 8 that reliably induced the differentiation signature, and furthermore yielded functional evidence of bona fide differentiation.

This data set contains HL-60 cells treated in a time course, in replicate, with 1 uM all trans retinoic acid (ATRA) and 10 nM phorbol 12-myristate 13-acetate (PMA). Also included are untreated HL-60 controls.  This data set was used to select marker genes that distinguish the undifferentiated from the PMA or ATRA differentiated states.
Keywords = AML
Keywords = leukemia
Keywords = HL-60
Keywords = chemical genomics
Keywords: repeat sample

first: Kimberly

last: Stegmaier

first: Kenneth

middle: N

first: Sierra

middle: A

last: Colavito

first: Shawn

last: O'Malley

first: Brent

last: Stockwell

first: Todd

last: Golub


title: Transcriptional studies on the deubiquitinating enzyme Ubp10

status: Public on Feb 01 2004

city: Milano

first: Marina

last: Vai

address: p.zza della Scienza 2

country: Italy

institute: Università degli Studi di Milano-Bicocca

summary:
Transcriptional analises of ubp10 null mutant, wild type and related null mutants.
Keywords = deubiquitinating enzymes
Keywords = yeast
Keywords: repeat sample

first: Ivan

last: Orlandi

first: Maurizio

last: Bettiga

first: Lilia

last: Alberghina


title: Extraocular, masticatory, and hindlimb muscles, comparison of putative muscle allotypes (Porter lab)

first: Henry

last: Kaminski

summary:
Extraocular Muscle is Defined by a Fundamentally Distinct Gene Expression Profile.  Adult mouse extraocular, masticatory, and hindlimb (gastrocnemius/soleus) muscles of adult mice were compared using Affymetrix microarrays.  Data form part of publication: Proceedings of the National Academy of Sciences USA 98:12062-12067, 2001.
Keywords: parallel sample

last: Porter


title: Rnt1 KO Sc and Wild-type BMA64 Sc

status: Public on Jul 19 2005

city: Los Angeles

first: Guillaume

middle: Francois

last: Chanfreau

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

summary:
Strain background is BMA64 with RNT1 gene deleted with the TRP marker Media is SD -Trp (synthetic dextrose minimal media missing tryptophan) Cells were grown until midlog and harvested at OD600=0.4; MAS5 (Statistical Algorithm) Scaling:All Probe Sets Target Signal 500;Normalization:All Probe Sets; Alpha1=0.04; Alpha2=0.06; Tau=0.015

Strain background is BMA64 with plasmid expressing TRP marker Media is SD -Trp (synthetic dextrose minimal media missing tryptophan) Cells were grown until midlog and harvested at OD600=0.4
; MAS5 (Statistical Algorithm) Scaling:All Probe Sets Target Signal 500;Normalization:All Probe Sets; Alpha1=0.04; Alpha2=0.06; Tau=0.015
Keywords: repeat sample

first: Albert

last: Lee

first: Anthony

middle: K

last: Henras


title: Myogenic differentiation_Cchip

status: Public on Jan 24 2004

city: Boston

first: Kinga

middle: Katarzyna

last: Tomczak

address: 300 Longwood Avenue

department: Genomics Program and Division of Genetics

institute: Children's Hospital Boston

summary:
In this study, Affymetrix MG_U74Av2 and MG_U74Cv2 GeneChips were used to analyze gene expression over a 12 day time course in C2C12 myoblasts induced to differentiate in vitro.  Triplicate cultures were studied during cell proliferation (days -2 and -1), at cell cycle withdrawal (day 0) and during myogenic fusion and maturation of multinucleated myotubes (days 2, 4, 6, 8, 10).  The manuscript associated to this work is Tomczak et al., FASEB J., 2003 Dec 19.  Additionally, the supplementary data can be found on our homepage at http://www.chb-genomics.org/beggslab/
Keywords = C2C12 myoblasts
Keywords = myogenesis
Keywords: time-course

first: Voichita

middle: D

last: Marinescu

first: Marco

last: Ramoni

first: Despina

last: Sanoudou

first: Federica

last: Montanaro

first: Mei

last: Han

first: Louis

last: Kunkel

first: Isaac

last: Kohane

first: Alan

last: Beggs


title: Oxidative stess in Drosophila heads

status: Public on Jan 18 2004

city: San Francisco

first: Sige

last: Zou

department: Physiology Department

institute: University of California, San Francisco

summary:
Profiled the effect of oxidative stress on gene expression in the heads of adult Drosophila.   The flies were fed sucrose with 15mM paraquat (experimental condition) or regular sucrose (control condition) for 30 hours, before harvesting at adult d3.
Keywords = oxidative stress
Keywords = paraquat
Keywords: dose response


title: Aging in heads from adult Drosophila males, w118 strain

summary:
The w1118 strain is an inbred lab stock widely used in genetic and transgenic studies.  w1118 males have a median life span of 35 days.

Adult males were collected within 24 hr after eclosion.  Approximately 200 flies were maintained in constant darkness in each food bottle at 25°C and 70% humidity and were transferred to fresh bottles every 3-4 days.   Transcripts were harvested at d3 and d47.

To separate the head from the rest of the body, flies were frozen and briefly vortexed in liquid nitrogen. Fly heads were collected using a sieve which retained fly bodies.  Total RNA was extracted using Trizol (GIBCO/BRL).  Poly(A) RNA was isolated using Oligotex resin (Qiagen).  Samples were profiled with Affymetrix DrosGenome1 GeneChips, using standard Affymetrix protocol.
Keywords: time-course


status: Public on Jan 01 2004

first: Bradley

last: Quade

address: 75 Francis Street

institute: Brigham and Women's Hospital

summary:
Comparison of Gene Expression in Uterine Smooth Muscle Tumors (including normal myometrium, benign uterine leiomyoma, malignant uterine and extra-uterine leiomyosarcoma. Total RNA was isolated with Trizol and converted to labeled cRNA by standard Affymetrix protocols. Before analysis, Avg Diff values were normalized to a sum of 3 million for each probe set on the chip and values less than 20 were adjusted to 20 to allow log scaling in subsequent analysis.
Keywords: other

first: George

middle: L

last: Mutter

first: Cynthia

middle: C

last: Morton


title: HS to HR progression

first: Charlie

last: Chen

institute: University of California at Los Angeles

summary:
Seven pairs of hormone sensitive and hormone refractory prostate cancer xenografts
Keywords: parallel sample

first: Charles

last: Sawyers


title: pediatric sarcoma: rhabdomyosarcoma & Ewing's sarcoma

status: Public on Mar 13 2004

first: Matthias

last: Nees

address: Im Neuenheimer Feld 156

department: Pediatric Oncology & Hematology

institute: Heidelberg University, Children's Hospital

summary:
Affymetrx U95Av2 GeneChip hybridizations, RNA extracted from primary human pediatric alveolar (aRMS) and embryonal (eRMS) rhabdomyosarcoma, plus primary pediatric Ewing's sarcoma (EWS)
Keywords = pediatric sarcoma
Keywords = Ewing's sarcoma
Keywords = rhabdomyosarcoma
Keywords: other

first: Claudia

last: Baer

first: Stephen

last: Breit

first: Barbara

last: Selle

first: Andreas

last: Kulozik

first: Karl-Ludwig

last: Schaefer

first: Yvonne

last: Braun

first: Daniel

last: Wai

first: Christopher

last: Poremba


title: Baseline replicates (ordered as hours -4, -3, -2, -1)

status: Public on Dec 19 2003

city: Providence

first: Boris

last: Gershman

state: RI

address: Attn: Marc Tatar, Box G-W

department: Ecology and Evolutionary Biology

institute: Brown University

summary:
Baseline replicates at start of time-course.  Flies in these samples were killed just prior to the start of both yeast (Y) and no yeast (NY) treatments (see below), i.e. at hour 0.  The four samples were temporally ordered as described for change-point analysis.

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition
Keywords: ordered

first: Lillian

last: Hang

first: Marc

last: Tatar


title: No Yeast (NY) Treatment Series

summary:
Hourly time course samples for the no yeast (NY) treatment group.  Note that the samples at hours 4 and 8 do not have microarray data due to insufficient RNA yield.

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast.  The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY).  Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments.  In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments.  Baseline replicates were temporally ordered as noted for change-point analysis.  No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen).  Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.  Microarray data was normalized by DNA-Chip Analyzer  (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition
Keywords: time-course


title: Yeast (Y) Treatment Series

summary:
Hourly time course samples for the yeast (Y) treatment group.

Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast. The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY). Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments. In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments. Baseline replicates were temporally ordered as noted for change-point analysis. No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen). Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol. Microarray data was normalized by DNA-Chip Analyzer (dChip, http://www.dchip.org), which utilizes an invariant difference selection (IDS) algorithm to construct a normalization relation.
Keywords = insulin, diet, nutrition
Keywords: time-course


title: Microarray Comparison Using Normal Human Colonic Mucosa

status: Public on Dec 14 2003

city: Kiel

first: Nancy

last: Mah

institute: Christian-Albrechts-University Kiel

summary:
This series represents a group of five samples (from sigmoid colon biopsies of clinically normal Patients A-E) profiled by a publicly available cDNA-based platform (GPL284) and a commercial oligonucleotide-based platform (GPL91).

Sample RNA extraction:

Biopsies taken during endoscopic analysis were immediately snap-frozen in liquid nitrogen and at no time prior to or during subsequent sample manipulation were the samples allowed to thaw.  Standard laboratory procedures to eliminate the presence of RNases, including the use of RNase free plastic-ware, heat baked glassware, molecular biology grade chemicals and DEPC-treated solutions, were adopted.  Frozen biopsies were crushed to a fine powder under liquid nitrogen using a manual crusher with a teflon head (Omnilab) and total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol, with minor modifications that improved RNA yields and purity in our hands.  In brief, crushed biopsy samples were lysed in an appropriate volume of Buffer RLT (typically 600 µL/20 mg tissue).  To facilitate complete lysis, samples were allowed to stand at room temperature for 5-10 min before vortexing.  The lysate was homogenized by addition to a QIA shredder column (Qiagen) and centrifuged at 14,000 rpm for 2 min.  The resulting supernatant was centrifuged at 14,000 rpm for 3 min to pellet any cell debris.  One volume of 70% ethanol was added to the cleared lysate, added to the RNeasy column and centrifuged at 10,000 rpm for 15 sec.  Bound RNA was washed with the addition of RW1 buffer to the column and allowed to stand at room temperature for 10 min followed by centrifugation at 10,000 rpm for 15 sec.  DNase 1 incubation mix (Stock: 273 kunits; RNase-free DNase Set, Qiagen) was added directly to the spin column membrane and digestion of any contaminating genomic DNA was carried out at room temperature for 30 min.  The column was washed with RWI buffer and the DNase treatment step was repeated.  The bound RNA was washed with RW1 buffer and centrifuged at 10,000 rpm for 15 sec three times, followed by two additional wash and centrifugation steps with RPE buffer.  Finally, purified RNA was eluted off the column with RNase-free water.  RNA concentration and purity was determined spectrophotometrically at A260/A280 and was determined to be intact as assessed by formaldehyde gel electrophoresis.  The presence of genomic DNA contamination was assessed by PCR amplification of GAPDH using standard PCR conditions and the following primers: GAPDH_F2-5’- ACCCACTCCTCCACCTTTGAC-3’, GAPDH_R2- 5’-CTGTTGCTGTAGCCAAATTCGT-3’. RNA was re-treated with DNase if necessary. Upon confirming the quality of the RNA (intact and free of genomic DNA), 15 µg of total RNA from each of the five biological replicates was used for expression screening on either the Affymetrix or the clone-based filter platform.
Keywords: parallel sample

first: Anders

last: Thelin

first: Tim

last: Lu

first: Susanna

last: Nikolaus

first: Tanja

last: Kühbacher

first: Yesim

last: Gurbuz

first: Holger

last: Eickhoff

first: Günther

last: Klöppel

first: Hans

last: Lehrach

first: Björn

last: Mellgård

first: Christine

last: Costello

first: Stefan

last: Schreiber

first: Nicola

last: Dierkes


title: Mesangioblast clone comparison- U74B

status: Public on Dec 25 2003

city: Modena

first: Enrico

last: Tagliafico

address: Via Campi 287

department: Center for Genome Research

institute: University of Modena and Reggio Emilia

summary:
Mouse dorsal aorta from E9.5 mouse embryos (C57BL6) was grown as an explant culture as described elsewhere (De Angelis et al., 1999). After 5 days the explant was dissociated into a single cell suspension, and plated at limiting dilution on a feeder layer of Mitomycin C-treated primary embryonic mouse fibroblasts, in 96 multiwell plates in complete medium, RPMI 20% Fetal Calf Serum. After 1 week, mesangioblast clones appeared approximately 2-4% of the wells. When the clones had grown to approximately 103 cells they were passed on gelatin-coated dishes, and further expanded. Clones D16 and D351 were used for microarray analysis.
Keywords: other

first: Silvia

last: Brunelli

first: Fernanda

last: De Angelis

first: Rossana

last: Tonlorenzi

last: Baesso

first: Sergio

last: Ferrari

first: Irene

last: Bozzoni

first: Stefano

first: Giulio

last: Cossu


title: Drosophila gliogenesis during early embryogenesis - wholemount experiments

status: Public on Oct 28 2003

city: Basel

first: Haiqiong

last: Montalta-He

address: Klingelbergstrasse 50/70

department: Developmental Neurobiology

country: Switzerland

institute: Institute of Zoology

summary:
We report here the application of magnetic cell separation in microarray experiment to understand Drosophila gliogenesis during early embryogenesis. At stage 11, neuroectodermal cells were labeled by a fusion transmembrane protein, mCD8-GFP, in the wild-type embryos as wells as in the embryos where glide/gcm was overexpressed. Following the cell dissociation, neuroectodermal cells were purified by using the commercial available anti-mCD8 microbeads. Microarray experiments based on prepared neuroectodermal cells from wild-type embryos verse glide/gcm overexpressed embryos at stage 11 have revealed 76 gene differentially regulated by overexpression of glide/gcm.
Among them, there are 11 genes have already been shown to be regulated by glide/gcm in the previous publications. Additionally, we have identified 4 more new glide/gcm-regulated genes by in situ hybridization or immunohistochemical staining. It is very convincing that reduction of the tissue complexity by cell purification leads to low false positives in microarray experiment.
Keywords: repeat sample


title: Yeast versus no yeast nutrition study

first: Boris

last: Gershman

summary:
Larvae were reared on standard diet until early third instar, at which time they were washed and transferred to standard diet lacking yeast. The animals remained on this diet until four days after emergence, when one group of adults was switched back to standard diet containing yeast (group Y) while another remained on the diet lacking yeast (group NY). Flies from both groups were killed every hour for the next twelve hours, creating 24 samples across the two treatments. In addition, four samples of flies were killed just before the start of the time course and used as baseline replicates for the no yeast (NY) and yeast (Y) treatments. Baseline replicates were temporally ordered as noted for change-point analysis. No yeast (NY) treatment samples at hours four and eight did not yield microarray data due to insufficient RNA.

Total RNA was extracted from whole animals using Trizol (Invitrogen). Sample processing and microarray hybridization/scanning were performed at the Brown University Center for Genetics and Genomics according to Affymetrix protocol.

Change-point Analysis Results Table:

Results of running change-point analysis on dChip normalized data. Normalized data was transformed into yeast (Y):no yeast (NY) signal ratios, and change-point analysis was performed by GeneTrace on these ratios (see publication for more information on change-point analysis).

Raw Data, Not Normalized Table:

Raw data (not normalized). Image files were analyzed by Affymetrix Microarray Suite (MAS) 5.0 with no normalization and no scaling. Signal abundance measurements, present [P], marginal [M], or absent [A] calls, and detection p-values reported were all produced by MAS 5.0. Note that there is no data for no yeast (NY) treatment samples at hours 4 and 8 due to insufficient RNA yield.
Keywords = insulin, diet, nutrition
Keywords: other

first: Lillian

last: Hang

first: Marc

last: Tatar


title: Amyotrophic lateral sclerosis

status: Public on Nov 14 2003

first: Fernando

last: Dangond

institute: Brigham and Women's Hospital Laboratories

summary:
Identification of amyotrophic lateral sclerosis (ALS) associated genes. Post mortem spinal cord grey matter from sporadic and familial ALS patients compared with controls.
Keywords: other

first: Robert

last: Brown

first: Steven

middle: R

last: Gullans


title: Mesangioblast clone comparison- U74C


title: Blood pulmonary arterial hypertension

status: Public on Nov 15 2003

city: Aurora

first: Christopher

last: Coldren

address: 12700 East 17th Place

institute: University of Colorado School of Medicine

summary:
Microarray analysis of peripheral blood mononuclear (PBMC) cells in pulmonary arterial hypertension.
Keywords = mononuclear cells
Keywords = gene microarray
Keywords = pulmonary arterial hypertension
Keywords = Herpesvirus
Keywords = biomarker
Keywords: other

first: Todd

last: Bull

first: Mark

last: Moore

first: Sylk

last: Sotto-Santiago

first: David

middle: V

last: Pham

first: Norbert

middle: F

last: Voelkel

middle: W

last: Geraci


status: Public on Oct 27 2003

summary:
We report here the application of magnetic cell separation in microarray experiment to understand Drosophila gliogenesis during early embryogenesis. At stage 11, neuroectodermal cells were labeled by a fusion transmembrane protein, mCD8-GFP, in the wild-type embryos as wells as in the embryos where glide/gcm was overexpressed. Following the cell dissociation, neuroectodermal cells were purified by using the commercial available anti-mCD8 microbeads. Microarray experiments based on prepared neuroectodermal cells from wild-type embryos verse glide/gcm overexpressed embryos at stage 11 have revealed 76 gene differentially regulated by overexpression of glide/gcm.
Among them, there are 11 genes have already been shown to be regulated by glide/gcm in the previous publications. Additionally, we have identified 4 more new glide/gcm-regulated genes by in situ hybridization or immunohistochemical staining. It is very convincing that reduction of the tissue complexity by cell purification leads to low false positives in microarray experiment.
Keywords: other


title: Drosophila gliogenesis during early embryogenesis - sorted experiment


title: angiogenesis

status: Public on Nov 28 2003

first: Cristin

last: Print

institute: Cambridge University

summary:
HUVECs (human umbilical cord vein endothelial cells) are treated with the angiogenic factors VEGF-A (vascular endothelial growth factor-A) and PlGF (placental growth factor) in low or high serum media.
Keywords: other


title: Idiopathic thrombocytopenic purpura (ITP)

status: Public on Aug 08 2003

city: Goteborg

first: Bob

last: Olsson

address: Vita Straket 10

country: Sweden

institute: Internal Medicine

summary:
CD3+ cells were studied in duplicate from healthy controls, patients with active ITP and ITP in remission.
Keywords: repeat sample


title: Differential Myocardial Gene Expression in the Development and Rescue of Murine Heart Failure

status: Public on Nov 02 2003

city: Durham

first: Burns

last: Blaxall

state: NC

institute: Duke University Medical Center

summary:
Numerous murine models of heart failure (HF) have been described, many of which develop progressive deterioration of cardiac function. We have recently demonstrated that several of these can be "rescued" or prevented by transgenic cardiac expression of a peptide inhibitor of the beta-adrenergic receptor kinase (betaARKct). To uncover genomic changes associated with cardiomyopathy and/or its phenotypic rescue by the betaARKct, oligonucleotide microarray analysis of left ventricular (LV) gene expression was performed in a total of 53 samples, including 12 each of Normal, HF, and Rescue. Multiple statistical analyses demonstrated significant differences between all groups, and further demonstrated that betaARKct Rescue returned gene expression toward that of Normal. In our statistical analyses, we found that the HF phenotype is blindly predictable based solely on gene expression profile. To investigate the progression of HF, LV gene expression was determined in young mice with mildly diminished cardiac function and in older mice with severely impaired cardiac function. Interestingly, mild and advanced HF mice shared similar gene expression profiles and, importantly, the mild HF mice were predicted as having a HF phenotype when blindly subjected to our predictive model described above. These data not only validate our predictive model, but further demonstrate that, in these mice, the HF gene expression profile appears to already be set in the early stages of HF progression. Thus, we have identified methodologies that have the potential to be used for predictive genomic profiling of cardiac phenotype, including cardiovascular disease.
Keywords: other

first: B

first: R

last: Spang

first: H

last: Rockman

first: W

last: Koch


title: Overexpression of dn-p21ras as a model system for severe dilated cardiomyopathy

status: Public on Oct 24 2003

first: Martina

last: Schinke

address: 7 Divinity Ave

department: Bauer Center for Genomic Research

institute: Harvard University

summary:
Mice heterozygous for dn-p21 littermates were sacrificed at 10 weeks of age. Ventricles were isolated and snap-frozen in liquid nitrogen.  Use 3 month old FVB Females as controls.  [GSM2334, GSM2335, GSM2336]
Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/ras_home.html
Keywords = ras
Keywords = dilated cardiomyopathy
Keywords: other

first: Tetsuo

last: Shioi

first: Lauren

last: Riggi

first: Seigo

last: Izumo

first: Iuan

last: Chen


title: Transcriptional response of lymphoblastoid cells to ionizing radiation

status: Public on Oct 08 2003

city: Philadelphia

first: Kuang-Yu

last: Jen

department: Department of Pediatrics and Genetics

institute: University of Pennsylvania

summary:
Time series for gene expression changes following 3 Gy and 10 Gy of ionizing radiation exposure.
Keywords: time-course

first: Vivian

middle: G

last: Cheung


title: Time course analysis of response to HCMV infection

status: Public on Sep 25 2003

city: Princeton

first: Thomas

last: Shenk

department: Department of Molecular Biology

institute: Princeton University

summary:
The effect of human cytomegalovirus infection
on cellular mRNA accumulation was analyzed by gene chip technology over a 48h time course
Keywords: time-course

first: Edward

middle: P

last: Browne

first: Bret

last: Wing

last: Coleman


title: Peripheral Blood Mononuclear Cells of Rhesus Macaques Infected with SIVmac251

status: Public on Jul 16 2003

city: Rockville

first: Maryanne

last: Vahey

state: MD

address: 1600 East Gude Drive

institute: Walter Reed Army Institute of Research

summary:
Using the Affymetrix HuGeneFL GeneChip, the global expression patterns of genes in the peripheral blood mononuclear cells (PBMCs) of rhesus macaques, infected with SIVmac251 and exhibiting rapid, typical, or slow rates of disease progression, were examined. Assessments of the change in gene expression (fold change), the temporal coordination of gene expression (self-organizing map analysis), and the similarities and significant differences in gene expression across the groups were performed on samples taken before infection and 3 and 7 weeks postinfection. An upregulation of the p27 interferon-inducible gene and of genes associated with cellular activation and immune response was observed in all three groups. Rapidly progressing animals exhibited a modest number of genes with a change in expression of 3-fold or greater, typically progressing animals exhibited the greatest number, and slowly progressing animals exhibited the fewest. Self-organizing map cluster analysis indicated that rapidly progressing animals exhibited the least coordinated gene expression over the three study time points, typically progressing animals exhibited a moderate degree, and animals with slow progression exhibited the most coordinated gene expression. Mann-Whitney U analysis indicated that differences in gene expression were most pronounced between the rapidly and slowly progressing groups and least pronounced between the rapidly and typically progressing animals. These observations elucidate distinct features of gene expression in animals with different rates of disease progression.
Keywords: other

first: M

middle: T

middle: E

last: Nau

last: Taubman

first: J

last: Yalley-Ogunro

first: P

last: Silvera

last: Lewis


title: CD34+ cell analysis

city: Seattle

first: Lynn

last: Graf

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary:
Comparison of gene expression in CD34+ cells from bone marrow and G-CSF-mobilized peripheral blood to investigate why the latter are optimal for allogeneic transplant recipients.
Keywords: other

first: Beverly

last: Torok-Storb

first: Heimfeld

last: Shelly

first: Shelly

last: Heimfeld


title: Mouse models of cardiac remodeling

status: Public on Aug 22 2003

first: Maria

last: Mirotsou

institute: Brigham and Women's Hospital, Harvard Medical School

summary:
We employed the Affymetrix GeneChip technology to evaluate the patterns of expression in two different in vivo models of cardiac remodeling and in two different regions (left ventricle free wall and septum) of the heart. Mice underwent transverse aortic constriction (TAC); myocardial infarction (MI) or Sham operation and RNA from the left ventricle free wall and the septum was isolated 1 week later.
Keywords: other


title: Granulosa cell tumorigenesis

city: Cleveland

first: John

middle: H

last: Nilson

address: 2109 Adelbert Road

department: Pharmacology

institute: Case Western Reserve University, School of Medicine

summary:
Comparison of global changes in ovarian transcriptomes uniquely associated with either granulosa cell tumors or luteomas, and identification of new markers for this tumor phenotype. Luteinizing hormone hypersecreting mice studied.
Keywords: other

first: Gabe

last: Owens

first: Ruth

last: Keri


title: Proliferating normal human peripheral blood mononuclear cells infected with HIV type 1 RF

summary:
Exploiting the power of high-density gene arrays, the simultaneous expression analysis of 5600 cellular genes was executed on proliferating peripheral blood mononuclear cells (PBMCs) from three normal human donors that were infected in vitro with the T cell tropic laboratory strain of HIV-1, RF. Profiles of expressed genes were assessed at 1, 12, 24, 48, and 72 hr postinfection and compared with those of matched uninfected PBMCs. Viral infection resulted in an overall increase in the number of genes expressed with peaks of expression at 1, 12, and 48 hr postinfection. Functional clustering of genes whose expression level in infected PBMCs varied by 2-fold or greater from levels in the controls indicated that cellular activation markers, proteins associated with immune cell function and with transcription and translation, exhibited increased expression subsequent to viral infection. Gene families exhibiting a decline in gene expression were confined to the 72 hr time point and included genes associated with catabolism and a subset of genes involved with cell signaling and synthetic pathways. Self-organizing map (SOM) cluster analysis identified temporal patterns of coordinated gene expression in infected PBMCs including genes associated with the immune response, the cytoskeleton, and ribosomal subunit structural proteins required for protein synthesis.
Keywords: other

first: L

last: Jagodzinski

first: N

last: Michael


title: E2F1-regulated genes

city: Tampa

first: William

middle: Douglas

last: Cress

state: FL

address: 12902 Magnolia Drive

department: Oncology

institute: Moffitt Cancer Center

summary:
Identification of E2F1-regulated genes that modulate the transition from quiescence into DNA synthesis, or have roles in apoptosis, signal transduction, membrane biology, and transcription repression.
Keywords: other


title: Response to LiCl of galactose grown cells

status: Public on Jun 23 2003

city: Kgs. Lyngby

first: Christoffer

last: Bro

address: Building 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

summary:
Wild type strain CEN.PK113-7D was grown in an aerobic batch cultivation with a start concentration of 20 g/L galactose. During exponential growth at a biomass concentration of 3 g dry weight/L LiCl was added to a concentration of 10 mM. Just before addition of LiCl (time 0) and 20, 40, 60 and 140 minutes after addition of LiCl samples were taken for transcription analysis. Lithium inhibits phosphoglucomutase whereby both galactose uptake and growth is strongly affected.
Keywords = Saccharomyces galactose lithium
Keywords: time-course

first: Birgitte

last: Regenberg

first: Gilles

last: Lagniel

first: Jean

last: Labarre

first: Mónica

last: Montero-Lomelí

first: Jens

last: Nielsen


title: NK2 model of congenital heart disease

status: Public on Jul 13 2003

city: Cambridge

first: Martina

last: Schinke

summary:
Lack of the conserved NK2-domain of the cardiac transcription factor Nkx2.5 causes multiple heart defects .

The NK2 family of homeobox genes constitutes a family of transcription factors that play an important role in different developmental processes. Members of this group are characterized by two highly conserved protein domains: the homeodomain, conferring DNA binding activity, and the NK2-specific domain (NK2-SD) of yet unknown function. One of the best characterized members of this group is the early cardiogenic marker Nkx2.5. Loss of function of Nkx2.5 leads to embryonic lethality around E10.5 due to an arrest of heart development at the looping stage. We have further dissected the function of Nkx2.5 in vivo by creating a knockout mouse line harboring an in frame deletion of the NK2-SD by Cre/loxP mediated excision. Homozygous mutant mice die at E14.5 due to severe cardiac malformations, e.g. common AV canal, DORV, and VSD. Lack of the NK2-SD leads to downregulation of the ventricular markers MLC-2v and Irx4 specifically in the right ventricle, and is accompanied with reduced right ventricular function. This function of Nkx2.5 seems to be independent of its ability to bind target DNA, since lack of the NK2-SD does not alter the DNA binding activity of Csx/Nkx2.5 in vitro. Heterozygous mutant mice show a spectrum of cardiac defects related to cardiac septation and valve morphogenesis, but lack conduction system defects as reported for heterozygous Nkx2.5 mice. The phenotype observed in NK2-SD mutant mice shows that Nkx2.5 is not only crucial during early steps of cardiogenesis but also plays an important role at later developmental stages.

Embryos were isolated at embryonic day 12.5. The entire embryo heart was taken and isolated in ice-cold PBS and immediately frozen on dry-ice. Total RNA was extracted from pooled samples of wildtype, heterozygous and mutant embryos.
Keywords = congenital heart disease, Csx, Nkx2.5
Keywords: other

first: Lauren

last: Riggi

first: Iuan-Bor

last: Chen

first: Seigo

last: Izumo


title: Calorie restriction and aging

city: Madison

first: Tsuyoshi

last: Kayo

state: WI

address: 445 Henry Mall

institute: University of Wisconsin-Madison

summary:
Gene expression profiles of kidney tissue from control-fed 5-month-old, control-fed 30-month-old and calorie restricted 30 month-old C57BL/6 mice.
Keywords = kidney, aging, calorie restriction
Keywords: other

first: T

first: Y

last: Higami

first: R

last: Weindruch

middle: A

last: Prolla


title: Yeast glucosamine treatment

status: Public on May 30 2003

first: Garrett

middle: M

last: Frampton

address: 9 Cambridge Center

department: Biology

institute: Whitehead Instute - MIT

summary:
We did transcription profiling on the effect of glucosamine in Saccharomyces cerevisiae using Research Genetics strains BY4741 (wild type) and 5251 (fks1). Yeast cells exposed to glucosamine in YPD growth medium show a significant increase in chitin content in the lateral cell wall. Likewise, cell wall stress caused by a gene deletion e.g., fks1 also results in elevated chitin. By comparing our data for fks1 with those from the literature we confirmed a strong induction of genes responsive to cell wall integrity, environmental stress as well as genes involved in cell signaling. Wild type cells treated with 15 mM glucosamine for 2 hours did not show any significant change in their transcription profile although the chitin level doubled during this time. For cells continuously exposed to glucosamine (steady state) there was a moderate transcription response, 105 genes showed a two-fold or higher change. The largest groups of up-regulated genes were those involved in mating, sporulation and cell cycle arrest. The largest group of down-regulated genes pertained to mitochondrial respiration. There was little overlap between those genes that have altered transcription from glucosamine treatment and those responsive to the fks1 mutation.
Keywords = saccharomyces chitin glucosamine
Keywords: parallel sample

first: Dorota

last: Bulik

first: Mariusz

last: Olczak

first: Hector

last: Lucero

first: Barbara

last: Osmond

first: Phillips

last: Robbins

first: Charles

last: Specht


title: Mouse EE uterine time course

status: Public on Apr 09 2003

city: East Lansing

first: Tim

last: Zacharewski

address: 223 Biochemistry Bldg.

department: Biochemistry & Molecular Biology, National Food Safety & Toxicol

institute: Michigan State University

summary:
Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1 mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Two replicates of each sample are provided. In addition, one time=0 sample is included.
Keywords = uterus estrogen time mouse
Keywords: time-course

first: K

last: Fertuck

first: J

last: Eckel

first: C

last: Gennings


title: Drosophila Eye Development - Larval Stage

status: Public on Jan 21 2003

first: Lydia

last: Michaut

address: Klingelbergstrasse 70

department: Cell Biology

institute: Biozentrum

summary:
Analysis of gene expression during  Drosophila eye formation.
Keywords: other

first: Susanne

last: Flister

first: Martin

last: Neeb

first: Kevin

last: White

first: Ulrich

last: Certa

first: Walter

middle: J

last: Gehring


title: Wing imaginal disc spatial expression

status: Public on Jan 08 2003

city: Columbus

first: Amanda

last: Simcox

address: 484 W 12th Ave

department: Molecular Genetics

institute: Ohio State University

summary:
Wing imaginal discs were dissected to generate body wall and wing/hinge fragments.  Targets from three biological replicates of each were generated and the expression profiles were determined using Affymetrix Drosophila Genechip 1 arrays.  Comparisons between the sample groups allow the identification of genes with localized expression patterns.
Keywords = Drosophila, wing disc, spatially restricted transcripts
Keywords: repeat sample

first: Miranda

last: Butler

first: Thomas

last: Jacobsen

first: Donna

last: Cain

first: Michael

last: Jarman

last: Hubank

first: Robert

middle: S

last: Whittle

first: Roger

last: Phillips

first: J Robert


title: T and B lymphocyte development profiles

status: Public on Jan 29 2003

city: Munich

first: Reinhard

last: Hoffmann

address: Trogerstr. 30

institute: Institute for medical microbiology

summary:
Expression profiles of seven consecutive stages of mouse thymocyte development were generated.  Previously known expression patterns of several genes were confirmed. Ten percent (1,304 of more than 13,000) of the monitored genes were found with 99% confidence to be differentially expressed across all T cell developmental stages. When compared with 1,204 genes differentially expressed in five consecutive B lineage developmental stages of bone marrow, >40% (546 genes) appeared to be shared by both lineages. However, when four pools of functionally distinct cell stages were compared between B and T cell development, DJ-rearranged precursor cells and resting immature precursor cells before and after surface Ag receptor expression shared less than 10%, mature resting lymphocytes between 15 and 20%, and only cycling precursors responding to precursor lymphocyte receptor deposition shared >50% of these differentially expressed genes.
Keywords: other

first: Ludovica

last: Bruno

last: Seidl

first: Antonius

last: Rolink

first: Fritz

last: Melchers

first: Ton


title: Large-scale analysis of the mouse transcriptome

status: Public on Dec 06 2002

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://biogps.gnf.org) that integrates data visualization and curation of current gene annotations.
Keywords: other

first: A

middle: I

last: Su

first: M

last: Cooke

first: K

last: Ching

first: Y

last: Hakak

first: J

first: T

last: Wiltshire

last: Orth

first: R

last: Vega

first: L

last: Sapinoso

last: Moqrich

last: Patapoutian

first: G

last: Hampton

first: P

last: Schultz

middle: B

last: Hogenesch


title: Inflammatory myopathy

status: Public on Feb 12 2003

city: Boston

first: Steven

middle: Alan

last: Greenberg

address: 75 Francis Street

department: Neurology

institute: Brigham and Women's Hospital

summary:
Molecular profiles of muscle tissue in patients with inflammatory myopathies
Keywords: other

first: S

first: D

last: Sanoudou

middle: N

last: Haslett

first: I

last: Kohane

last: Kunkel

last: Beggs

last: Amato


title: Expression profiling by p53 status

status: Public on Nov 25 2002

city: Chapel Hill

first: Fred

last: Wright

department: Biostatistics

institute: University of North Carolina

summary:
Human colorectal carcinoma-derived cell lines, p53 -/-, +/-, +/+ at 0 and 12 hrs after growth arrest.
Keywords = p53, expression, colon cancer, CSPG2
Keywords: repeat sample

first: Heejei

last: Yoon

first: Sandya

last: Liyanarachchi

first: Ramana

last: Davuluri

first: Janet

middle: C

last: Lockman

first: Albert

last: de la Chapelle

first: Natalia

last: Pellegata


title: Yeast aging study

status: Public on Jun 03 2003

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary:
Wild type and sgs1 null yeast were grown under DNA damaging (with MMS) conditions or without treatment to log phase and their transcriptional profiles compared .

The human aging diseases Werner and Bloom syndromes are a result of mutation of the WRN and BLM genes, respectively. The SGS1 gene of Saccharomyces cerevisiae is homologous to the human WRN and BLM genes of the RecQ DNA helicase family. Deletion of SGS1 results in accelerated yeast aging and a reduction in life span as well as cell cycle arrest. We demonstrate that SGS1 deletion, DNA damage, and stress show similar transcriptional responses in yeast. Our comparative analysis of the genome-wide expression response of SGS1 deletion, stress and DNA damage indicates parallel transcriptional responses to cellular insult and aging in yeast.
Keywords: other

last: Sambandan

first: C

last: Rha


title: Bladder tumour recurrence prediction

status: Public on Dec 08 2002

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

institute: Aarhus University Hospital, Skejby

summary:
Expression profiling of superficial bladder tumours to delineate the expression pattern differences between non-recurring and recurring tumours.
Keywords = bladder cancer, superficial, recurrence, prediction
Keywords: other

first: Thomas

last: Thykjaer

first: Mogens

last: Kruhoffer

first: Jens

middle: L

last: Jensen

first: Niels

last: Marcussen

first: Stephen

last: Hamilton-Dutoit

first: Hans

last: Wolf

first: Torben

middle: F

last: Orntoft


title: Insulin resistant muscle sample pool 5

status: Public on Aug 26 2002

city: Phoenix

first: Paska

last: Permana

state: AZ

department: Phoenix Epidemiology and Clinical Research Branch

institute: NIDDK, NIH

summary:
Muscle sample pool #5 from 2 insulin resistant subjects.
Keywords: parallel sample

first: Xiaolin

last: Yang

first: Richard

last: Pratley

last: Tokraks

first: Clifton

last: Bogardus


title: Type 2 diabetes and insulin resistance

status: Public on Dec 17 2002

summary:
Global transcript profiling to identify differentially expressed skeletal muscle genes in insulin resistance, a major risk factor for Type II (non-insulin-dependent) diabetes mellitus.  Compared gene expression profiles of skeletal muscle tissues from 18 insulin-sensitive versus 17 insulin-resistant equally obese, non-diabetic Pima Indians.
Keywords: other

first: X

first: R

first: S

first: P


title: Insulin resistant muscle sample pool 3

summary:
Muscle sample pool #3 from 4 insulin resistant subjects.
Keywords: parallel sample


title: Insulin resistant muscle sample pool 4

summary:
Muscle sample pool #4 from 3 insulin resistant subjects.
Keywords: parallel sample


title: Bladder tumour stage classification

summary:
Bladder tumours used to construct a tumour stage classifier
Keywords = bladder cancer, disease stages, classification
Keywords: other


title: Insulin resistant muscle sample pool 1

summary:
Muscle sample pool #1 from 4 insulin resistant subjects.
Keywords: parallel sample


title: Insulin resistant muscle sample pool 2

summary:
Muscle sample pool #2 from 4 insulin resistant subjects.
Keywords: parallel sample


title: Comparison of Dorsal threshold outputs

status: Public on Nov 27 2002

city: Berkeley

first: Angelike

last: Stathopoulos

address: 401 Barker Hall

department: Molecular and Cellular Biology

institute: University of California

summary:
Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo.

The maternal Dorsal regulatory gradient initiates the differentiation of several tissues in the early Drosophila embryo. Whole-genome microarray assays identified as many as 40 new Dorsal target genes, which encode a broad spectrum of cell signaling proteins and transcription factors. Evidence is presented that a tissue-specific form of the NF-Y transcription complex is essential for the activation of gene expression in the mesoderm. Tissue-specific enhancers were identified for new Dorsal target genes, and bioinformatics methods identified conserved cis-regulatory elements for coordinately regulated genes that respond to similar thresholds of the Dorsal gradient. The new Dorsal target genes and enhancers represent one of the most extensive gene networks known for any developmental process.
Stathopoulos et al., Cell, Vol 111, 687-701, November 2002.
Keywords: repeat sample

first: Madeleine

last: Van Drenth

first: Michael

last: Levine


title: Effect of dietary oils on hippocampus and liver gene expression

status: Public on Nov 11 2002

city: Lausanne

first: David

last: Vilanova

institute: Nestle Research Center

summary:
Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression.

Brain:

GSM2558: Control

GSM2559: Control

GSM2560: Fungal oil (AA)

GSM2561: Fungal oil (AA)

GSM2562: Fish oil (DHA)

GSM2563: Fish oil (DHA)

GSM2564: Fish and Fungal oil (DHA + AA)

Liver:

GSM2565: Control

GSM2566: Control

GSM2567: Control

GSM2568: Control

GSM2569: Fungal oil (AA)

GSM2570: Fungal oil (AA)

GSM2571: Fish oil (DHA)

GSM2572: Fish oil (DHA)

GSM2573: Fish + Fungal oil (DHA +AA)

GSM2574: Fish + Fungal oil (DHA +AA)

Keywords: ordered

first: A

last: Berger

first: D

last: Mutch

first: B

last: German

first: Matthew-Alan

last: Roberts


title: Insulin sensitive muscle sample pool 4

summary:
Muscle sample pool #4 from 3 insulin sensitive subjects.
Keywords: parallel sample

first: Stephen


title: Insulin sensitive muscle sample pool 2

first: Paska

summary:
Muscle sample pool #2 from 4 insulin sensitive subjects.
Keywords: parallel sample


title: Normal human muscle

status: Public on Aug 21 2002

city: Rochester

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

summary:
RNA from vastus lateralis of healthy young (21-31 year old) and older (62-77 year old) men. Signal data normalized to mean intensity of 500 over all probes sets. Analysis done with Affymetrix Microarray Suite 5.0 software.
Keywords: other

first: Charles

last: Thornton

first: Andrew

last: Brooks


title: Pressure-Overload Induced Cardiac Hypertrophy

status: Public on Jul 30 2002

first: Martina

last: Schinke

address: 7 Divinity Ave

department: Bauer Center for Genomic Research

institute: Harvard University

summary:
Aortic banding is an excellent model system to evaluate the process of development of left ventricular hypertrophy in response to hemodynamic stress.  The Affymetrix GeneChip MgU74Av1 was used to analyze expression profiles of mice at different time points after surgical intervention for pressure-overload induced hypertrophy.  More information about this model may be obtained at  http://cardiogenomics.med.harvard.edu/groups/proj1/pages/band_home.html
Keywords = Pressure overload, cardiac hypertrophy
Keywords: time-course

first: Lauren

last: Riggi

first: Iuan

last: Chen

first: Seigo

last: Izumo


title: Insulin sensitive muscle sample pool 5

last: Permana

summary:
Muscle sample pool #5 from 4 insulin sensitive subjects.
Keywords: parallel sample

first: Xiaolin

last: Yang

first: Richard

last: Pratley

last: Tokraks

first: Clifton


title: Insulin sensitive muscle sample pool 3

summary:
Muscle sample pool #3 from 3 insulin sensitive subjects.
Keywords: parallel sample

last: Bogardus


title: Mammary epithelial cell transduction

status: Public on May 16 2003

city: Los Angeles

first: Hilary

last: Coller

address: Terasaki Life Science Building 5145, 610 Charles E Young Drive E

institute: University of California, Los Angeles

summary:
Analysis of gene expression in mammary epithelial cells transduced with either hTERT, empty LXSN vector or empty BABE vector.
Keywords: other


title: FVB Benchmark Set for Cardiac Development, Maturation, and Aging

summary:
The Affymetrix GeneChip MgU74Av1 was used to analyze expression profiles of mice at different developmental stages to monitor changes in cardiac gene expression over time.  More information about this model may be obtained at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/fvb_home.html
Keywords = Cardiac development
Keywords: time-course


title: Congenital heart disease in Csx/ Nkx2.5 mutant embryos

status: Public on Aug 02 2002

summary:
We have developed gene-targeted mice with deletion of Nkx2.5.  Embryos were isolated at embryonic day 9.5 and the middle third containing the heart was run on Affymetrix  Mu11kA and Mu11kB arrays.  For more information about this model see
http://cardiogenomics.med.harvard.edu/groups/proj1/pages/csx_home.html
Keywords = Congenital heart disease
Keywords: other


title: Insulin sensitive muscle sample pool 1

summary:
Muscle sample pool #1 from 4 insulin sensitive subjects.
Keywords: parallel sample


title: Murine bone marrow B cell precursors

status: Public on Jan 09 2002

first: Reinhard

last: Hoffmann

summary:
Affymetrix GeneChip derived gene expression profiles of flow sorted murine B cell precursors, ex-vivo isolated, RNA-amplified
Keywords = RNA amplification, B cell development, oligonucleotide arrays
Keywords: ordered

first: Thomas

last: Seidl

first: Martin

last: Neeb

first: Antonius

last: Rolink

first: Fritz

last: Melchers

first: Ton