title: Hepatic gene expression profiling of GH transgenic coho salmon with and without ration restriction

first: Matthew

middle: Lawrence

last: Rise

address: 600 E. Greenfield Ave.

department: Great Lakes WATER Institute

institute: University of Wisconsin - Milwaukee

summary:
This is the first use of cDNA microarrays to study the influence of GH transgenesis on liver gene expression in a non-mammalian vertebrate.  Three groups of salmon were examined: transgenic on full ration (T), transgenic on restricted ration (R), and control nontransgenic (C).  Daily weight gains in T were approximately 8-fold higher than in C, and 4-fold higher than in R.  Differential gene expression in T, R, and C samples was determined using ~ 16,000 gene microarrays.  In the GRASP microarray studies, only those features (cDNA spots on the microarrays) behaving similarly (e.g. greater than 2-fold up-regulated in T relative to C) in all slides of the study will be reported to minimize false positives occurring due to dye bias and technical variability.  Coho salmon transcripts responding reproducibly to GH transgenesis with and without feed rationing will be reported.  Many of the microarray-identified hepatic transcripts responsive to GH transgenesis with and without rationing are involved in iron homeostasis, metabolism, cellular proliferation, and innate immunity.
Keywords: Impact of growth hormone transgenesis with and without ration restriction on global hepatic gene expression

overall_design: Differential gene expression in R (ration-fed GH transgenic), T (ration-fed GH transgenic) and C (control non-transgenic) coho salmon liver samples was determined using the 16,006 gene (16K) GRASP cDNA microarrays.  For each 16K microarray comparison (C vs. T, C vs. R, or T vs. R), 2 slides were hybridized (1 chip and 1 dye flip).  Therefore, there were six slides total in this study.  The C vs. T comparison consisted of slide EB017.061 (Cy3 = C, Cy5 = T) and its dye flip EB017.066 (Cy3 = T, Cy5 = C).  The C vs. R comparison consisted of slide EB017.063 (Cy3 = R, Cy5 = C) and its dye flip EB017.064 (Cy3 = C, Cy5 = R).  The T vs. R comparison consisted of slide EB017.062 (Cy3 = T, Cy5 = R) and its dye flip EB017.065 (Cy3 = R, Cy5 = T).

first: Susan

middle: E

last: Douglas

first: Dionne

last: Sakhrani

first: K

middle: V

last: Ewart

first: Jason

last: Williams

first: Marlies

first: William

last: Davidson

first: Ben

middle: F

last: Koop

first: Robert

last: Devlin


title: Comparative Transcript Abundance in E. Coli Degradosome Mutants and their Parental Strains

status: Public on Jan 06 2006

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

summary:
Comparative transcript abundance in E. Coli degradosome mutants and their parental strains.
Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes.
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out.
Keywords: genetic_modification_design

overall_design: Computed

first: Sue

last: Lin-Chao


title: Molecular profiling of anemia in acute renal allograft rejection

summary:
Compromised renal function after renal allograft transplantation often results in anemia in the recipient. Molecular mechanisms leading to anemia during acute rejection are not fully understood; inadequate erythropoietin production and iron deficiency have been reported to be the main contributors. To increase our understanding of the molecular events underlying anemia in acute rejection, we analyzed the gene expression profiles of peripheral blood lymphocytes (PBL) from four pediatric renal allograft recipients with acute rejection and concurrent anemia, using DNA microarrays containing 9000 human cDNA clones (representing 7469 unique genes). In these anemic rejecting patients, an 'erythropoiesis cluster' of 11 down-regulated genes was identified, involved in hemoglobin transcription and synthesis, iron and folate binding and transport. Additionally, some alloimmune response genes were simultaneously down-regulated. An independent data set of 36 PBL samples, some with acute rejection and some with concurrence of acute rejection and anemia, were analyzed to support a possible association between acute rejection and anemia. In conclusion, analysis using DNA microarrays has identified a cluster of genes related to hemoglobin synthesis and/or erythropoeisis that was altered in kidneys with renal allograft rejection compared with normal kidneys. The possible relationship between alterations in the expression of this cluster, reduced renal function, the alloimmune process itself, and other influences on the renal transplant awaits further analysis.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Keywords: disease_state_design

overall_design: Using regression correlation

first: Minnie

last: Sarwal


title: Chemosensitivity prediction of Paclitaxel-Platinum combination therapy by expression profile in ovarian cancer

status: Public on Dec 31 2005

city: Hiroshima

first: Keiko

last: Hiyama

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

country: Japan

institute: Hiroshima University

summary:
Ten human ovarian cancer cell lines were kindly provided as follows: an ovarian serous adenocarcinoma cell line, SKOV3 (Dr. N. Nagai, Hiroshima University, Hiroshima, Japan); KF28 and its TXL/CDDP-resistant variant (Dr. Y. Kikuchi, National Defense Medical College, Saitama, Japan); KF, SHIN3 and 5 ovarian clear cell adenocarcinoma cell lines, KK, TAYA, RMG-1, OVISE and OVTOKO (Dr. M. Suzuki, Jichi Medical School, Tochigi, Japan). All cell lines were cultured in RPMI 1640 medium (Life Technologies, Inc., Grand Island, NY) containing 10% heat-inactivated fetal bovine serum (FBS; BioWhittaker, Verviers, Belgium) in a humidified atmosphere of 5% CO2 and maintained in continuous exponential growth by passage every 3 days.
Exponentially growing cultured cells were collected after two-washings with PBS. The cell pellets were immediately frozen in liquid nitrogen, and stored until use. Total RNA was extracted using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA). The quality of the RNA was checked using Agilent Technologies 2100 Bioanalyzer (Agilent, Palo Alto, CA).
CodeLink Expression Bioarray System (Amersham Bioscience, Tokyo, Japan) was used according to the manufacturer’s protocol. Briefly, first-strand cDNA was generated from 1 microgram of total RNA of each cell line using reverse transcriptase and a T7 primer, and then second-strand cDNA was produced using DNA polymerase mix and RNase H.  Complementary RNA (cRNA) was generated via an in vitro transcription reaction using T7 RNA polymerase and biotin-11-UTP (Perkin Elmer, Boston, MA), which was quantified by spectrometry and checked using Agilent Technologies 2100 Bioanalyzer (Agilent). Ten-microgram of cRNA was then fragmented and hybridized to a Uniset Human 20K I Bioarray containing 19,881 probes with positive and negative bacterial control probes. After hybridization, the arrays were rinsed and labeled with Streptavidin-Cy5, scanned using Agilent DNA Microarray Scanner (Agilent), then analyzed with CodeLink Expression Analysis Software ver.2.3. Expression levels were normalized to the median expression value of the whole array spots.
Keywords: parallel sample

overall_design: To explore the candidates of drug sensitivity determinants and fix formulae to predict resistance to anticancer drugs, expression profiles of 10 ovarian cancer cell lines were obtained using oligonucleotide microarray analysis and compared with sensitivity to anticancer drugs, paclitaxel and cisplatin, measured by MTT assay.

first: Masahiko

last: Nishiyama

first: Masaaki

last: Komatsu

first: Keiji

last: Tanimoto


title: Comparison of Campylobacter jejuni isolates implicated in Guillain-Barre syndrome and strains that cause enteritis

status: Public on Jan 04 2006

summary:
We asked whether Campylobacter jejuni isolated from patients with Guillain-Barri syndrome (GBS) differ from isolates isolated from patients with uncomplicated gastrointestinal infection using DNA microarray analysis. We found that specific GBS genes or regions were not identified, and microarray analysis confirmed significant genomic heterogeneity among the isolates.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Edward

last: Leonard


title: Chemosensitivity prediciton in esophageal cancer cell line using cDNA microarray

summary:
A total of 20 KYSE human esophageal squamous cell carcinoma cell lines (KYSE-30, -140, -150, -170, -180, -200, -220, -350, -410, -450, -510, -520, -590, -770, -850, -890, -1170, -1190, -1250, and -2270) and a non-cancerous esophageal epithelial cell (HEEC-1)were kindly provided by Dr. Y. Shimada (Kyoto University, Kyoto, Japan).  The KYSE cell lines were cultured in RPMI 1640 medium (Life Technologies, Inc., Grand Island, NY) containing 10% heat-inactivated fetal bovine serum (FBS; BioWhittaker, Verviers, Belgium) in a humidified atmosphere of 5% CO2 and maintained in continuous exponential growth by passage every 3 days. HEEC-1 cells were cultured in Keratinocyte SFM medium with growth supplement containing 2.5 mg EGF and 25 mg bovine pituitary extract in 500 mL liquid basal medium (GIBCO BRL, Rockville, MD) and expanded by passage twice in a week. The exponentially growing cultured cells (2 x 10^6) were collected after two-washings with PBS. Total RNA was prepared from the frozen cell pellets using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA), and mRNA was purified using MACS mRNA Isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the supplier’s protocols.
RIKEN human 21K array containing 20,784 clones with positive and negative controls was used to analyze gene expression of 20 KYSE esophageal cancer cell lines using HEEC-1 as reference. The target DNAs used to construct human 21 K array were the glycerol stock of cDNA clones purchased from ResGen (Invitrogen Corporation, Carlsbad, CA)). One-microgram poly(A) RNAs from KYSE cells and the reference cells were labeled with Cy3-dCTP and Cy5-dCTP, respectively, by random-primed reverse transcription. Arrays were laser-scanned using ScanArray 5000TM confocal laser scanner (GSI Lumonics, Billerica, MA), and the images were analyzed using ScanAlyzeTM (Stanford University). All experiments were performed in duplicate (_1 & _2).
Keywords: parallel sample

overall_design: To explore the genes responsible for chemosensitivity in cancer cells, expression profiles of various cancer cell lines were examined. Statistically comparing them with the chemosensitivity measured by in vitro MTT assay in each cell line, several candidate genes were selected and predicition models for anticancer efficacy were established using their expression levels.

first: Tatsushi

last: Shimokuni

last: Otani

first: Megu

last: Ohtaki

first: Yasushi

last: Okazaki

first: Yoshihide

last: Hayashizaki


title: Resistant response of leaves of upland cotton line Im216 to Xanthomonas campestris pv. malvacearum race 1

status: Public on Jan 01 2006

city: Stillwater

first: Margaret

last: Essenberg

state: OK

address: 246 NRC, OSU

department: Biochemistry & Mol. Biol.

institute: Oklahoma State University

summary:
Gene expression profiling of upland cotton line Im216 to inoculation with Xanthomonas campestris pv. malvacearum race 1.
Fifth or sixth leaves of the bacterial blight-resistant cotton line Im216, which had been grown in a plant growth chamber, were infiltrated with a suspension of about 5x10^6 colony-forming units ml^-1 of Xanthomonas campestris pv. malvacearum race 1 in sterile saturated CaCO3 solution or were not inoculated (control).
Keywords: Time-course

overall_design: Samples consisting of one leaf were harvested at 8, 14, 20, 30, 45, and 60 hpi.  Three biological replicate experiments were performed on separate occasions.  Total RNA was isolated, and from each sample 50 µg was reverse-transcribed along with non-plant normalizing Sp4 RNA (0.5 ng) and Sp5 RNA (0.05 ng), hybridized to slides for approximately 18 h, and detected with Cy5 (inoculated) or with Cy3 (non-inoculated) labeled dendrimers (hybridization for 3 h), using the 3DNA Array 350TM kit (Genisphere).  Hybridization signals were measured using a ScanArray Express (PerkinElmer), and images were processed with GenePix Pro version 4.0 (Axon Instruments).  Normalized log ratio VALUES were determined using the R-project statistical environment (<http://www.r-project.org/>), Bioconductor (<http://www.bioconductor.org/>) and the LIMMA package (Smyth 2004) through the GenePix AutoProcessor (GPAP, http://darwin.biochem.okstate.edu/gpap/>) website (H. Weng and P. Ayoubi, unpublished).

first: Mohini

middle: A

last: Patil

middle: L

last: Pierce

first: Angela

last: Phillips

first: Bryan

middle: J

last: Venters

first: Patricia

last: Ayoubi

first: Hua

last: Weng


title: Comparison between naïve, tolerant and memory CD8+ T cells

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
To elucidate transcriptional differences between naïve, tolerant and memory CD8+ T cells, genome-wide gene expression profiling was performed.  The indicated cell populations were purified from immunized or naïve Rag-/- TCR mice by cell sorting and RNA was extracted labeled and hybridized to an Affymetrix custom mouse array GNF1M GeneChip.  RNA from sorted samples was prepared, split into two aliquots prior to making labeled cDNA, so that two arrays were used for each cell population.Alterations in transcript levels were determined through pair wise comparisons of naïve cells to either memory or tolerant CD8+ T cells.
Keywords: cell type

overall_design: duplicates consisted of replicate aliquots of the same total RNA

first: Ryan

middle: M

last: Teague

first: Blythe

middle: D

last: Sather

first: Jilian

last: Sacks

first: Maria

middle: Z

last: Huang

first: Michelle

last: Dossett

first: Junko

last: Morimoto

first: Susan

last: Sutton

first: Michael

middle: P

last: Cooke

first: Xiaoxio

last: Tan

first: Claes

last: Öhlén

first: Philip

last: Greenberg


title: transfer_spores_to_YPD

status: Public on Jan 25 2006

city: Rehovot

first: Naama

last: Barkai

address: P.O box 26

country: Israel

institute: Weizmann Institute

summary:
We have used genome-wide expression profiling to investigate how budding yeast cells become committed to sporulation. Sporulating cells were transferred to growth medium at different stages of the process, and their transcription response was characterized. Most sporulation-induced genes were immediately down-regulated upon the transfer, even in committed cells that continued to sporulate. The metabolic-related transcription response of pre-committed cells or of mature spores transferred to growth medium was essentially the same as that of vegetative cells exposed to glucose. In contrast, committed cells elicited a unique, and dramatically different response. Our results suggest that cells ensure commitment to sporulation not by stabilizing the process, but by modulating their information processing in an active manner that may optimize sporulation in an environment-specific manner.
Keywords: Time course

overall_design: Wild type SK1 cells (DS1) were grown to saturation in YPD (2% yeast extract, 4% bactopeptone, 4% glucose) for 24 hours and plated on sporulation plates (0.25% yeast extract, 1.5% Potassium acetate, 0.05% glucose supplemented with all amino acids).  3 days old asci were harvested and suspended in YPD at 30?C to initiate spore germination. RNA for microarray hybridization was extracted at the indicated times.


title: Contribution of unique genes by individual cell lines to Universal Mouse Reference RNA

status: Public on Jan 05 2006

last: Stanford Microarray Database

summary:
RNA from 11 individual mouse cell lines were reverse-transcribed to cDNA, labeled with Cy5 and cohybridized with Cy3-labeled UMRR onto 7,500-spot mouse oligo microarrays (UNC). The data was analyzed using GeneTraffic software. 300-1000 spots out of 8,000 were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics on only one microarray was determined.
A reference experiment design type is where all samples are compared to a common reference.
Keywords: reference_design

first: Charles

last: Perou


title: Chemosensitivity prediction in esophageal cancer cell line using oligonucleotide array

first: Keiko

last: Hiyama

summary:
A total of 20 KYSE human esophageal squamous cell carcinoma cell lines (KYSE-30, -140, -150, -170, -180, -200, -220, -350, -410, -450, -510, -520, -590, -770, -850, -890, -1170, -1190, -1250, and -2270) were kindly provided by Dr. Y. Shimada (Kyoto University, Kyoto, Japan).  The KYSE cell lines were cultured in RPMI 1640 medium (Life Technologies, Inc., Grand Island, NY) containing 10% heat-inactivated fetal bovine serum (FBS; BioWhittaker, Verviers, Belgium) in a humidified atmosphere of 5% CO2 and maintained in continuous exponential growth by passage every 3 days. The exponentially growing cultured cells (2 x 10^6) were collected after two-washings with PBS. Total RNA was prepared from the frozen cell pellets using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA). The quality of the RNA was checked using Agilent Technologies 2100 Bioanalyzer (Agilent, Palo Alto, CA).
CodeLink Expression Bioarray System (Amersham Bioscience, Tokyo, Japan) was used according to the manufacturer’s protocol. Briefly, first-strand cDNA was generated from 1 µg of total RNA for each cell line using reverse transcriptase and a T7 primer, and then second-strand cDNA was produced using DNA polymerase mix and RNase H. cRNA was generated via an in vitro transcription reacrion using T7 RNA polymerase and biotin-11-UTP (Perkin Elmer, Boston, MA). After quantified by spectrometry and qualified using Agilent Technologies 2100 Bioanalyzer (Agilent), 10 µg of cRNA was fragmented and hybridized to a Uniset Human 20K I Bioarray containing 19,981 human probes with 108 positive and 300 negative bacterial control probes. After hybridization, the arrays were rinsed and labeled with Streptavidin-Cy5, scanned using Agilent DNA Microarray Scanner (Agilent), then analyzed with CodeLink Expression Analysis Software ver.2.3. Expression levels were normalized to the median expression value of the whole array spots except for the bacterial controls.
Keywords: parallel sample

first: Masahiko

last: Nishiyama

first: Tatsushi

last: Shimokuni

first: Keiji

last: Tanimoto

first: Eiso

last: Otani

first: Megu

last: Ohtaki


title: Gene expression profiles of whole blood incubated with live meningococci

status: Public on Dec 30 2005

summary:
Blood from two donors was incubated for timepoints up to 24 hours in the presence and absence of live meningococci. The donors are labelled NP and SW. 'SWB' refers to blood that was incubated with meningococci; 'Unstim' refers to control blood incubated in the absence of meningococci.  Duplicate arrays were prepared for the majority of timepoints ('a' and 'b'), except where the array of of poor quality and not used in the analysis.
We infected heparinised whole blood from two healthy donors (adult volunteers) with 108 live meningococci, serogroup B, type MC58, as previously described.8 Blood was incubated at 37°C for 0, 1, 3, 6, 12, and 24 h. At every timepoint we removed a sample and harvested the plasma by centrifugation (1200 g, 10 min). We gathered the remaining blood into RNA stabilisation fluid. Uninfected control blood was obtained for every timepoint.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Cheryl

last: Hemingway

first: Stephen

last: Popper


title: D11.5 Tubular Porcine Conceptus

city: Beltsville

first: Le Ann

last: Blomberg

state: MD

address: 10300 Baltimore Ave.

department: ANRI

institute: ARS-USDA

summary:
Transcriptome profiling of  in vivo-derived porcine conceptus at the tubular stage (12-80 mm) during the elongation period of peri-implantation development.
Keywords: Embryo stage of development

overall_design: Transcriptome profiling of in vivo derivied porcine conceptuses at critical stages of pre-implantation development is being investigated to ascertain gene expression profiles associated with competent embryo development.

first: LeAnn

first: Kurt

last: Zuelke


title: Cell type and culture condition-dependent alternative splicing in human breast cancer cells

city: Duarte

first: Ren-Jing

last: Lin

address: 1500 E. Duarte Rd.

department: Molecular Biology

institute: Beckman Research Institute

summary:
We used splicing-sensitive microarrays to
detect differences in alternative splicing between two breast cancer cell lines MCF7 (estrogen receptor positive) and MDA-MB-231 (estrogen receptor negative), as well as cultured human mammary epithelial cells (HMEC). Several splicing alterations in genes,
including CD44, FAS, RBM9, HnRNPA/B, APLP2, and MYL6, were detected by the
microarray, and verified by RT-PCR. We also compared splicing in these breast cancer cells cultured in either two-dimensional flat dishes (2-D) or in three-dimensional Matrigel (3-D) conditions. Only a subset of the splicing differences that distinguish MCF7 cells from MDA-MB-231 cells under 2-D culture condition is retained under 3-D conditions, suggesting that alternative splicing events are influenced by the geometry of the culture conditions of these cells.
Keywords: Splicing-sensitive microarray

overall_design:
The design of oligonucleotides is for the general detection of splicing variants from a given gene. The junction oligonucleotides consist of exon?exon junction sequence, because different splice variants will have different exon?exon junctions. The microarray also
contains oligonucleotides that are complementary to flanking constitutive
exons, and the alternative exon. This splicing-sensitive microarray was used
because a signal derived from the hybridization to the constitutive exon oligonucleotides would, in theory, reflect the total amount of RNA from the particular gene, whereas hybridization signals from an exon-exon junction oligonucleotide would reflect the amount of RNA containing that particular junction. The ratio of hybridization
intensity from an oligonucleotide spanning a specific exon-exon junction to that from a constitutive exon oligonucleotide would provide information about the level of that
alternatively spliced RNA in the two comparison samples. Using this type of splicingsensitive array, one can acquire two sets of information from one array: expression level changes for the gene and changes in the distribution of the splice variants. The array used
in this study contained 64 genes that underwent alternative splicing, including estrogen receptor 1 and 2 (ER1 and ER2), CD44 (cell adhesion molecule), ITGA6 (integrin a6 precursor), FAS, LARD, WT1 (Wilm?s tumor protein 1),
and TP73 (tumor suppressor p73). Each gene could contain one or more simple
alternative exons, or more complex arrangements of multiple alternative exons.

first: Chunxia

last: Li

first: Mitsuo

last: Kato

first: Lily

last: Shiue

first: John

last: Shively

first: Manuel

last: Ares

first: Ren-Jang


title: Effects of methylseleninic acid on prostate cancer cells

status: Public on Dec 29 2005

last: Stanford Microarray Database

summary:
This set of arrays contains 31 experiments. It is designed to determine the effects of methylseleninic acid on the transcriptional program of prostate cancer LNCaP cells. Threee concentrations, 3, 10, and 30 uM, were used for treatment. The effects were monitored through a time course of 48 hours, with samples collected at 10 different time points (1, 2, 4, 6, 9, 12, 15, 18, 24, and 48). RNA from treated cells were labeled using Cy5, and untreated using Cy3. One experiment using RNA from untreated cells in both channel was used as control.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Keywords: compound_treatment_design

first: Hongjuan

last: Zhao


title: Response to high hydrostatic pressure

summary:
S. cerevisiae Y440 Mat a leu2 was grown in YEPD at 28 degrees C with aeration to exponential growth phase and was subjected to a hydrostatic pressure of 50 and 200 MPa for 30 minutes at room temperature. Total RNA was extracted using phenol/chloroform and further precipitated with 3 M sodium acetate / absolute ethanol. Extracted RNA samples were treated for 10 min with 0.5 U of RNAse-free DNAse I / ]g RNA at 37 oC to remove any residual genomic DNA. RNA pellets were washed in 70 % ethanol and resuspended in DEPC treated water. Purified mRNA from pressurized and unpressurized cells was reversed-transcribed, labeled with fluorescent-tagged nucleotides, and hybridized against a common refernce pool of mRNA for 18 h at 65 0C on cDNA microarray. After several washes, arrays were scanned using a commercially available scanning laser microscope (GenePix 4000) from Axon Instruments (Foster City, CA), the data obtained was normalized (mean value) applying a linear regression method.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract
Keywords: Computed


title: Analysis of mRNA expression profiles in bovine endometrium during the pre-attachment period

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary:
The endometrium plays a central role among the reproductive tissues in the context of early embryo-maternal communication and pregnancy. This study investigated transcriptome profiles of endometrium samples from Day 18 pregnant vs. non-pregnant heifers to get insight into the molecular mechanisms involved in conditioning the endometrium for embryo attachment and implantation. Using a combination of subtracted cDNA libraries and cDNA array hybridization 109 mRNAs with at least twofold higher abundance in endometrium of pregnant animals and 70 mRNAs with higher levels in the control group were identified. Among the mRNAs with higher abundance in pregnant animals at least 41 are already described as induced by interferons. In addition, transcript levels of many new candidate genes involved in regulation of transcription, cell adhesion, modulation of the maternal immune system, and endometrial remodeling were found as increased. The different expression level was confirmed with quantitative real-time PCR for nine genes. Localization of mRNA expression in the endometrium was shown by in situ hybridization for AGRN, LGALS3BP, LGALS9, USP18, PARP12, and BST2. A comparison with similar studies in humans and mice revealed species-specific and common molecular markers of uterine receptivity.
Keywords: Comparison of endometrium of pregnant versus control animals

overall_design: Endometrial tissue samples of day 18 pregnant cows (n=4) were compared to non-pregnant controls (n=6). First, subtracted cDNA libraries were produced enriched for cDNAs of genes upregulated either in pregnant animals (18KB) or in the controls (18KO). 1536 clones of every library were picked and PCR-amplified cDNA fragments were spotted on a separate array, respectively. These two arrays were then simultaneously hybridized with P-33 labeled probes derived from the 10 tissue samples (10 hybridizations, 18KB and 18KO array together in 1 hybridization vial). Differentially expressed cDNA clones in comparison of the pregnant and the non-pregnant control group were detected with SAM (Significance analysis of microarrays, Tusher et al. 2001) according to the following parameters: fold-change = 2; FDR = 1%. Signals of these cDNA clones were manually evaluated to eliminate false-positive signal differences. The differentially expressed cDNA clones and some additional interesting cDNA clones were sequenced.

first: Karin

last: Gross

first: Susanne

last: Schmidt

first: Hendrik

last: Wenigerkind

first: Helmut

last: Blum

first: Eckhard

last: Wolf


title: Profiling of Salmo salar in two Atlantic salmon types, a wild type versus transgenic.

city: Halifax

first: Jason

last: Williams

state: Nova Scotia

address: 1411 Oxford Street

department: Institute for Marine Biosciences

country: Canada

institute: National Research Council

summary:
The influence of GH transgenesis on liver gene expression in coho salmon was examined. Gene expression in livers of transgenic salmon on a restricted ration (R) was compared to that in livers of nontransgenic control salmon (C).
Keywords: Transcript profile

overall_design:
Livers of five size-matched salmon were preserved in RNALater (Ambion) and mRNA was prepared using the FastTrack kit (Invitrogen).  mRNA was quantified and quality-checked by spectrophotometer and agarose gel.  The microarray experiment used 100 ng of pooled mRNA templates:  pooled C contained equal quantities from 5 individual C fish, and pooled R contained equal quantities from 5 individual R fish.  All experiments were conducted in quadruplicate (2 replicates and 2 dye flips).
Preparation of cDNA using the SuperSmart PCR cDNA Synthesis Kit (BD Biosciences), amplification using the Advantage 2 PCR kit Kit (BD Biosciences), labeling of cDNA with Cy3- and Cy5-dCTP (Amersham), hybridization, and scanning were performed as previously described  (Tsoi et al., 2003; Ewart et al., 2005).  Normalization and data analysis was carried out using the GeneTrafficTM software (Iobion Informatics). Background fluorescence was subtracted from the spot intensities and spots were flagged and removed from the data set the signal to background ratio was less than 1, the signal to average background ratio was less than 1, or the signal intensity was less than 1000.  Data were normalized on a sub-grid basis using both locally weighted non-linear regression (Loess) and intensity-based methods. In addition, significance analysis of microarrays (SAM) was carried out on the normalized data to identify differentially regulated genes based on their changes in expression in relation to the standard deviation for multiple measurements.

first: Susan

last: Douglas

first: Bob

last: Devlin

first: Vanya

last: Ewart


title: T cell Basal Signaling

summary:
Signal transduction pathways guided by cellular receptors commonly exhibit low-level constitutive signaling in a continuous, ligand-independent manner. The dynamic equilibrium of positive and negative regulators establishes such a tonic signal. Ligandindependent signaling by the precursors of mature antigen receptors regulates development of B- and T-lymphocytes. Here we describe a basal signal controlling gene expression profiles in the Jurkat T cell line and mouse thymocytes. Using DNA microarrays and Northern blots to analyze unstimulated cells, we demonstrate that expression of a cluster of genes, including RAG-1 and RAG2, is repressed by constitutive signals requiring the adapter molecules LAT and SLP-76. This TCR-like pathway results from constitutive low-level activity of Erk and Abl kinases. Inhibition of Abl by the drug STI-571 or events upstream of Erk increases RAG-1 expression. Our data suggest that physiologic gene expression programs depend upon tonic activity of signaling pathways independent of receptor ligation.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Arsenic-induced changes in gene expression in the neural tube of Folr2-/- KO mouse embryos

city: Houston

first: Bogdan

last: Wlodarczyk

state: TX

address: 2121 W Holcombe Blv.

department: CEGM

institute: IBT

summary:
In order to more thoroughly investigate the mechanism of arsenate-induced NTDs we designed experiment in which highly sensitive Folr2 nullizygous mice were treated i.p. with teratogenic dose of sodium arsenate just at the beginning of the neural tube formation process. This specific knockout mouse and arsenic exposure conditions were chosen as they warranted high incidence of exencephaly in exposed embryos. We investigated the gene expression changes induced by arsenic in the anterior part of neural tube in order to discover patterns that might shed light on the mechanism of arsenic’s teratogenicity.
Keywords: toxic response

overall_design: On GD 7:12 and 8:12, pregnant Folr2-/- KO dams were injected ip with water solution of sodium arsenate at the dose of 9.6 mg As/ kg of body weight(treated) or with water for injection only (control). At three selected time-points: 8:15 (3 hours post-injection), 9:00 (12 hours post-injection) and 9:12 (24 hours post-injection), at least 4 control and arsenic treated dams were sacrificed and embryos harvested. From these embryos, the anterior part of neural tube was dissected and RNA extracted. No less than 6 embryonic neural tubes (3controls and 3 arsenic treated) for each time-point were used for hybridization on commercially available CodeLink UniSet 10K Bioarray. Together, 22 control and treated samples at above mentioned, 3 selected time-points were used in this study

first: Robert

last: Cabrera

first: Daniel

last: Bozinov

first: Denise

last: Hill

first: Richard

last: Finnell


title: A dual-genome microarray for the pea aphid, and its obligate bacterial symbiont

city: Tucson

first: Nancy

last: Moran

state: AZ

address: Biosciences West, Room 310, 1041 E. Lowell St.,  The University of Arizona

department: Ecology and Evolutionary Biology

institute: University of Arizona

summary:
Background:
The best studied insect-symbiont system is that of aphids and their primary bacterial endosymbiont Buchnera aphidicola.  Buchnera inhabits specialized host cells called bacteriocytes, provides nutrients to the aphid and has co-speciated with its aphid hosts for the past 150 million years.  We have used a single microarray to examine gene expression in the pea aphid, Acyrthosiphon pisum, and its resident Buchnera.  Very little is known of gene expression in aphids, few studies have examined gene expression in Buchnera, and no study has examined simultaneously the expression profiles of a host and its symbiont.  Expression profiling of aphids, in studies such as this, will be critical for assigning newly discovered A. pisum genes to functional roles.  In particular, because aphids possess many genes that are absent from Drosophila and other holometabolous insect taxa, aphid genome annotation efforts cannot rely entirely on homology to the best-studied insect systems.  Development of this dual-genome array represents a first attempt to characterize gene expression in this emerging model system.

Results:
We chose to examine heat shock response because it has been well characterized both in Buchnera and in other insect species.  Our results from the Buchnera of A. pisum show responses for the same gene set as an earlier study of heat shock response in Buchnera for the host aphid Schizaphis graminum.  Additionally, analyses of aphid transcripts showed the expected response for homologs of known heat shock genes as well as responses for several genes with unknown functional roles.

Conclusions:
We examined gene expression under heat shock of an insect and its bacterial symbiont in a single assay using a dual-genome microarray.  Further, our results indicate that microarrays are a useful tool for inferring functional roles of genes in A. pisum and other insects and suggest that the pea aphid genome may contain many gene paralogs that are differentially regulated.
Keywords: Stress response

sample_organism:
Buchnera aphidicola
Acyrthosiphon pisum

platform_organism:
Buchnera aphidicola
Acyrthosiphon pisum

overall_design: Two biological replicates (TUC1 and TUC2), dye-flip experiment

first: Alex

middle: C

last: Wilson

first: Helen

last: Dunbar

first: Gregory

middle: K

last: Davis

first: Wayne

middle: B

last: Hunter

first: David

last: Stern


title: Seasonal variation in leafy spurge crown bud gene expression

city: Fargo

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary:
These experiments were designed to follow the seasonal changes in the transcriptome of field-grown leafy spurge crown buds. The goal was to identify specific signaling pathways and marker genes characteristic to the changes that occur when the buds transitioned from paradormancy through endodormancy and into ecodormancy.
Keywords: Time course seasonal dormancy

platform_organism:
Manihot esculenta
Euphorbia esula

overall_design: We used a balanced dye swap, common reference design with two biological samples (collected monthly from Aug-Dec. in 2001 and again in 2003).

first: James

last: Anderson

first: Mauricio

last: Soto-Suárez

first: Wun

middle: S

last: Chao


title: BAC CGH array profiling using Phi29-amplified colon mucosa of microdissected samples from APC and MYH mutation carriers.

status: Public on Dec 25 2005

city: Lisbon

first: Joana

last: Cardoso

address: Av. Prof Egaz Moniz

country: Portugal

institute: Faculty of Medicine

type: Genome variation profiling by genome tiling array

summary:
Details of the series are available in the publication Cardoso J. et al., “Chromosomal instability in MYH- and APC-mutant adenomatous polyps”, Cancer Research, accepted for publication. Abstract of the publication: “The vast majority of colorectal cancers display genetic instability, either in the chromosomal (CIN) or microsatellite (MIN) forms. While CIN tumors are per definition aneuploid, MIN colorectal cancers, caused by loss of mismatch repair function, are usually near-diploid. Recently, bi-allelic germline mutations in the MYH gene, were found to be responsible for MAP (MYH associated polyposis), an autosomal recessive predisposition to multiple colorectal polyps, often indistinguishable from the dominant FAP (familial adenomatous polyposis) syndrome caused by inherited APC mutations. Here, we analyzed MYH- and APC-mutant polyps by combining laser-capture microdissection, isothermal genomic DNA amplification, and array-CGH (comparative genomic hybridization). Smoothed quantile regression methods were applied to the MAP and FAP genomic profiles to discriminate chromosomes predominantly affected by gains and losses. Up to 80% of the MAP polyps showed aneuploid changes, which is significantly higher than the 60% found among FAP polyps. Both MAP and FAP adenomas were characterized by frequent losses at chromosome 1p, 17, 19 and 22, and gains affecting chromosome 7 and 13. The observation that aneuploidy is already detectable at early stages of MYH-driven tumorigenesis raises the possibility that CIN may contribute significantly to accelerated tumor progression, increased cancer risk, and poor prognosis in MAP.”
Keywords: repeat, BAC, CGH

overall_design: Details of the series are available in the publication Cardoso J. et al., "Chromosomal instability in MYH- and APC-mutant adenomatous polyps", Cancer Research 2006 Mar 1;66(5):2514-9.

first: Lia

middle: X

last: de Menezes

first: Monique

last: van Leerdam

first: Carla

last: Rosenberg

first: Gabriela

last: Moslein

first: Julian

last: Sampson

first: Hans

last: Morreau

first: Judith

last: Boer

first: Riccardo

last: Fodde


title: Daphnia magna DNA microarray for the evaluation of toxicity of environmental chemicals

city: Okazaki

first: Hajime

last: Watanabe

state: Aichi

address: 5-1, Higashiyama

department: Center for Integrative Bioscience

institute: National Institutes of Natural Sciences

summary:
Toxic chemical contaminants have variety of detrimental effects on various species and the impact of pollutants on ecosystems has become an urgent issue.  However, very limited species have been examined to date and those studies are mainly limited to vertebrates.  In this study, we aimed to establish an ecotoxicogenomic bases for Daphnia magna.  Based on a daphnia EST database, we made oligonucleotide-based DNA microarray that has high reproducibility.  The DNA microarray was applied to evaluate gene expression profiles of daphnid exposed to chemicals.  Characteristic gene expression patterns depending on chemicals indicate that the Daphnia microarray can be used for mechanistic understanding of chemical toxicity.  Although acute toxicity test or reproductive toxicity test can provide hazardous concentrations of chemicals, they give no information about mode of action.  Our study can be a breakthrough for the evaluation of chemical toxicity on environmental organisms.
Keywords: Chemical response

overall_design:
Daphnia neonates were picked up within 24 h and they were exposed to chemicals for 24 h.  Chemicals used in this study were CuSO4, H2O2, pentachlorophenol and beta-naphthoflavone.
Number of replicates is 3.

first: Eri

last: Takahashi

first: Shigeto

last: Oda

first: Norihisa

last: Tatarazako

first: Taisen

last: Iguchi


title: Growth phase-dependent response of Helicobacter pylori to iron starvation.

status: Public on Dec 22 2005

last: Stanford Microarray Database

summary:
This data set was used to determine genes that are regulated by iron availability and to access the growth phase dependence on that regulation.  Stationary (Stat Chelate and Stat.iron.survival)and exponential (Log Chelate and Log.iron.survival)were subjected to chelation using DPP.  Growth status of the cultures was confirmed by determing the correlation coefficient of the Stat chelate T=0/control and Log Chelate T=0/control vs data generated in the TC Motility series.  Arrays used for iron addback experiments are listed as FeAddBack-1-time or FeAddBack-2-time.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Douglas

last: Merrell

first: Lucinda

last: Thompson


status: Public on Dec 21 2005

summary:
Transcriptome analysis of Arabidopsis colonized by a plant-growth promoting rhizobacterium reveals a general effect on disease resistance  RNA transcript levels of Arabidopsis plants, infected by the rhizobacterium Pseudomonas thivervalensis (strain MLG45), and axenic control plants were compared using cDNA microarrays representing approximately 14 300 genes. The analysis revealed an increase of defence-related transcripts in the shoots of bacterized plants relative to control (axenic) plants. These modifications of transcript levels were confirmed by physiological experiments. Plants infected with P. thivervalensis were more resistant to subsequent infections by the virulent pathogen P. syringae pv. tomato (strain DC3000) than control plants. In addition, photosynthesis rates were repressed consistently with the reduced growth of plants colonized by P. thivervalensis. These results highlight the value of molecular phenotyping to predict physiological changes.
Set of arrays that are part of repeated experiments
Keywords: Biological Replicate

overall_design:
Biological Replicate
Computed

first: Laurent

last: Nussaume


title: Skeletal muscle and insulin regulated genes

summary:
Insulin action in target tissues involved precise regulation of gene expression. To define the set of insulin-regulated genes in human skeletal muscle, we analyzed the global changes in mRNA levels during a 3-h hyperinsulinemic euglycemic clamp in vastus lateralis muscle of six healthy subjects. Using 29,308 cDNA element microarrays, we found that the mRNA expression of 762 genes, including 353 expressed sequence tags, was significantly modified during insulin infusion. 478 were up-regulated and 284 down-regulated. Most of the genes with known function are novel targets of insulin. They are involved in the transcriptional and translational regulation (29%), intermediary and energy metabolisms (14%), intracellular signaling (12%), and cytoskeleton and vesicle traffic (9%). Other categories consisted of genes coding for receptors, carriers, and transporters (8%), components of the ubiquitin/proteasome pathways (7%) and elements of the immune response (5.5%). These results thus define a transcriptional signature of insulin action in human skeletal muscle. They will help to better define the mechanisms involved in the reduction of insulin effectiveness in pathologies such as type 2 diabetes mellitus, a disease characterized by defective regulation of gene expression in response to insulin.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Karine

last: Clement


title: 3-Methylcholanthrene treated Rat

city: Madison

first: Aaron

last: Vollrath

state: WI

address: 1400 University Ave

institute: McArdle Laboratory

summary:
Analysis of transcriptional response changes in rats after treatment with 3-Methylcholanthrene
Keywords: toxicity

overall_design: Rats were treated with 3-methylcholanthrene (MC) (100 umol/kg) in corn oil (CO) (2 ml/kg), or were given equal volumes of CO, i.p., once daily for 4 days.  At 1, 15, and 28 day time points, the animals were sacrificed, and livers were stored at -800 C for later isolation of RNA.  Gene expression was studied by cDNA microarray analyses.  The analyses was conducted in the laboratory of Dr. Chris Bradfield of the University of Wisconsin.  Gene expression was monitored using 4572 unique clones from liver-derived EST libraries fortified with clones of known liver genes representing ~4000 genes.  These cDNAs represented toxicologically relevant genes such as drug metabolizing enzymes (e.g. P450s), inflammatory responsive genes (e.g. SAA-1), and genes that were previously identified as useful in classification of chemicals.  All clones were then sequence verified from both 3’ and 5’ directions.  Six replicates of each cDNA were printed on each array using a Microgrid II (Biorobotics, Woburn, MA).   The labeled cDNA from both the MC-treated groups and from a pool of the corresponding controls were mixed and hybridized to the liver microarray for 18 h according to the Genisphere (Hatfield, PA) protocol, as described in EDGE, a scientific resource for toxicology-related gene expression information (University of Wisconsin, Madison)

first: Bhagavatula

last: Moorthy


title: very moderate exercise training; variations in stress and toxicity gene expression in rat hearts.

status: Public on Dec 28 2005

city: Bologna

first: Marina

last: Marini

address: V. Belmeloro, 8

department: Histology, Embryology and Applied Biology

country: Italy

institute: University of Bologna

summary:
Array analysis of a set of 96 stress and toxicity genes was carried out in left ventricular cardiomyocytes from 8 control and 7 trained rats. The training protocol was very gradual and mild. Animals were sacrificed 48 hrs after the last training session in order to evaluate gene expression during the "second window of cardioprotection".
Array results were validated by Real Time PCR of selected genes and Western Blot analysis of selected proteins. Plasma MDA and resistance to ischemia/reperfusion were evaluated as well.
A total of 11 genes were found to be upregulated by moderate exercise, 3 to be downregulated. MDA was found to be increased in plasma of trained rats. Myocardial resistance to ischemia-reperfusion was found to be improved in trained rats with respect to controls.
Results suggest that such a pattern of mild training does at the same time elicit stress responses, but also the upregulation of a number of defensive genes, that are likely to constitute the core of the adaptive mechanisms.
Keywords: exercise training-related stress response and cardioprotection

overall_design:
Male albino Sprague-Dawley rats  entered the study at 2 months of age.
After one week of acclimatization, eight animals were randomly chosen for exercise training. The exercise was produced on a specific treadmill for rats, with four lanes. The training protocol was aimed at providing a gradually increasing effort to reach 50 % VO2max in 11 weeks; such workload was sustained for a further 3 wks. Animals were trained 1hr /day 3 times a week. Control animals were placed on a non-moving treadmill during the training sessions.
Animals were sacrificed 48 hrs after the last training session. Rats were anesthetized (100 mg/kg ip heparinized sodium thiopental); for RNA preparation hearts were removed and immediately frozen in liquid nitrogen and stored at -80°C. According to the original design, the sample size of control and trained animals was the same (8 control and 8 trained rats), but 1 trained rat died for reasons unrelated to the training procedure.
Frozen cardiac tissue (n= 8 control and 7 trained rats)  was reduced to powder by means of a sterilized ceramic mortar and pestle. RNA isolation was obtained by TRIZOLTM  (Invitrogen s.r.l., Milan, Italy), as suggested by the manufacturer.
The absence of RNA degradation was assessed by evaluation of 28S and 18S band sharpness after denaturing electrophoresis. The absence of contaminating genomic DNA was confirmed by PCR analysis with tubulin promoter-specific primers.
To control for inter-individual variation, an equivalent mass of total RNA from each subject in the group was pooled to generate the total RNA sample for probe generation. Synthesis of  Biotin-16-dUTP labeled cDNA probes was obtained with the use of AmpoLabeling-LPRTM Kit (SuperArray, Bioscience Corporation, Frederick, USA). In order to minimize false signals, for each RNA pool (control or trained rats), three replicas were made , with independent labeling and hybridizations procedures, so that six arrays were prepared. The Stress and Toxicity-focused Arrays (GEArray Q SeriesTM, SuperArray) were employed. Signal was developed by a chemiluminescent method (alkaline phosphatae-conjugated streptavidin and  CDP-Star®) and detected by exposing the membranes to X-ray film Kodak X-Omat AR (Sigma-Aldrich) .
The images from the arrays were scanned, acquired in a PC and analyzed using the software provided by ScanAlyze (eisen@genome.stanford.edu). Minimum spot intensity was used for automatic background subtraction. Data were then normalized with respect to the housekeeping gene RPL13a, one of the positive controls in the array. The three results obtained for each gene were averaged to give an expression score.
Other evaluations reported in Summary and contributing to the interpretation of array data (myocardial morphology, ischemia-reperfusion) were carried out on additional rats that were trained and handled in the same way and at the same time as those employed for the array study.

first: Rosa

last: Lapalombella

first: Vittoria

last: Margonato

first: Raffaella

last: Ronchi

first: Michele

last: Samaja

first: Cristina

last: Scapin

first: Luisa

last: Gorza

first: Paolo

last: Carinci

first: Carlo

last: Ventura

first: Arsenio

last: Veicsteinas


title: Scleroderma Architecture Cell Lines

last: Stanford Microarray Database

summary:
The data from these cell lines is described in figure 2 of the mansucript "Systemic and cell-type specific gene expression patterns in scleroderam skin" by Whitfield et al. (2003) PNAS.  Aortic smooth muscle cells and microvascular endothelial cells were obtained from Clonetics and cultured in the recommended media; Hs578T myofibroblast-like cells were grown in RPMI-1640 supplemented with phenol red, glutamine (2 mM) and 5% fetal calf serum; HeLa S3 epithelial cells were obtained from the American Type Culture Collection (ATCC) and cultured as described in Whitfield et al., MBC, (2002). Normal, morphea and scleroderma fibroblasts were derived from normal, morphea and scleroderma skin biopsies taken by Dr. Kari Connolly at UCSF.  In all cases, RNA was prepared from cells 48 hrs after changing the culture media to avoid the induction of serum responsive genes.  Poly(A) RNA from each cell line was reverse-transcribed into Cy5-dUTP (Amersham Pharmacia Biotech, Piscataway NJ) labeled cDNA and reference RNA reverse-transcribed into Cy3-dUTP (Amersham Pharmacia Biotech, Piscataway NJ) labeled cDNA using standard methods. Cells grown in culture were analyzed on cDNA microarrays containing 40,512 elements representing 28,384 UniGene clusters (UniGene Build No. 155, released 9-28-2002) manufactured in the Stanford Microarray Facility (http://www.microarray.org). Equal amounts of Cy5- and Cy3-labeled cDNA were hybridized to spotted cDNA microarrays and scanned using a GenePix 4000A Scanner (Axon Instruments, Union City CA). Detailed protocols are available at http://brownlab.stanford.edu/protocols.html/. Data were extracted by superimposing a grid over each array using GenePix 3.0 software (Axon Instruments, Union City CA). Spots of poor quality, determined by visual inspection, were excluded from further analysis.
A cell type comparison design experiment design type compares cells of different type for example different cell lines.
Keywords: cell_type_comparison_design

overall_design: Computed

first: Michael

last: Whitfield

first: Jen-Tsan

last: Chi


title: Baseline gene transcription in genital fibroblasts

summary:
To gain insights into the role of androgen in genital morphogenesis, we compared basal transcriptional patterns in genital fibroblasts from 46,XY individuals with either wild-type AR or germline inactivation of the AR as a result of mutation.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Keywords: disease_state_design

first: Paul-Martin

last: Holterhus


title: Bleomycin exposed lymphoblastoid cells

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

summary:
The uncovering of genes involved in susceptibility to the sporadic cancer types is a great challenge. It is well established that the way in which an individual deals with DNA damage is related to the chance to develop cancer. Mutagen sensitivity is a phenotype that reflects an individual’s susceptibility to the major sporadic cancer types, including colon, lung and head and neck cancer. A standard test for mutagen sensitivity is measuring the number of chromatid breaks in lymphocytes after exposure to bleomycin. The aim of the present study was to search for the pathways involved in mutagen sensitivity. Lymphoblastoid cell lines of seven individuals with a low mutagen sensitivity were compared with seven with a high score. RNA was isolated from cells exposed to bleomycin (4 hr) and unexposed cells. Micro-array analysis (19K) was used to compare gene expression of insensitive and sensitive cells. The profile of most altered genes after bleomycin exposure, analyzed in all fourteen cell lines, included genes involved in multiple processes, most prominent in cell proliferation and DNA repair. When comparing the insensitive and sensitive individuals other differentially expressed genes were found, that were involved in proliferation (e.g. BUB1) and signal transduction (e.g. DUSP4). This difference in expression profiles between mutagen sensitive and insensitive individuals justifies further studies aiming to elucidate the genes responsible for the development of sporadic cancers.
Keywords: exposure to dna damaging agent, comparison of phenotypic response to dna damaging agent

overall_design: We analyzed 14 lymphoblastoid cell lines without and with exposure to bleomycin for 4hr. Seven of these fourteen were insensitive to bleomycin, meaning that few chromatide breaks were examined after exposure to bleomycin. The other seven were sensitive, meaning that in these cell lines a relatively high number of chromatide breaks could be detected after exposure to bleomcyin.

first: Jacqueline

last: Cloos

first: Wim

last: de Boer

first: Mireille

middle: H

last: Snel

first: Paul

last: van den IJssel

first: Bauke

last: Ylstra

first: C

last: Leemans

first: Ruud

last: Brakenhoff

first: Boudewijn

last: Braakhuis


title: Effects of androgen treatment on genital fibroblasts

city: Stanford

address: 300 Pasteur Drive

institute: Stanford Microarray Database (SMD)

summary:
e tested the responses of normal and AIS genital fibroblasts to dihydrotestosterone (DHT), under culture conditions similar to those that were reported to produce aromatase induction in these cells [8]. Cells were treated with DHT (100-1,000 nM) both at confluency (G0) and during exponential growth, and transcript levels were assessed using DNA microarrays.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Keywords: compound_treatment_design


title: Scleroderma Morphea Normal Fibroblasts

summary:
Fibroblast were isolated from either back or forearm punch biopsies taken by Dr. Kari Connolly(UCSF) from either normal control patients, patients with a diagnosis of Systemic Sclerosis with Diffuse Scleroderma and patients with a diagnosis of morphea.  Scleroderma fibroblast were grown to confluence, media was changed and the RNA prepared from the cells 48 hrs later (to avoid serum responsive genes).
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Keywords: disease_state_design

overall_design: User Defined


title: Undifferentiated and differentiated mammosphere SAGE libraries

status: Public on Dec 20 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary:
Undifferentiated mammosphere RNA. Samples contain RNA extracted from the cells of mouse mammospheres. Mammosphere are believed to be comprised of stem/progenitor cells (GSM88038).
Differentiated mammosphere RNA. RNA extracted from the cells of mouse mammospheres induced to differentiate over a 6-day period. Mammosphere are believed to be comprised of stem/progenitor cells (GSM88039).
Keywords: mammosphere differentiation

overall_design: this experiment includes 2 samples


title: An Arabidopsis Mutant Resistant to Thaxtomin A, a Cellulose Synthesis Inhibitor from Streptomyces Sp

summary:
Thaxtomin A is a phytotoxin produced by Streptomyces scabies and other Streptomyces species, the causative agents of common scab disease in potato and other taproot crops. At nanomolar concentrations, thaxtomin causes dramatic cell swelling, reduced seedling growth, and inhibition of cellulose synthesis in Arabidopsis. We identified a mutant of Arabidopsis, designated txr1, that exhibits increased resistance to thaxtomin as a result of a decrease in the rate of toxin uptake. The TXR1 gene was identified by map-based cloning and found to encode a novel, small protein with no apparent motifs or organelle-targeting signals. The protein, which has homologs in all fully sequenced eukaryotic genomes, is expressed in all tissues and during all developmental stages analyzed. Microarray transcript profiling of some 14,300 genes revealed two stomatin-like genes that were expressed differentially in the txr1 mutant and the wild type. We propose that TXR1 is a regulator of a transport mechanism
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out.
Keywords: genetic_modification_design

first: Laurent

last: Zimmerli


title: ICAT quantitative proteomic analysis of Myc-induced apoptosis

city: San Antonio

first: Yuzuru

last: Shiio

address: 8403 Floyd Curl Dr.

department: CCRI

institute: UTHSCSA

summary:
Quantitative proteomic analysis of Myc-induced apoptosis in serum-deprived Rat1_Myc fibroblasts. Mitochondrial, chromatin, and soluble fractions analyzed.

Original peptide data contained in Supplementary files.
Keywords: proteomic, apoptosis, cell fractions

overall_design: Rat1_Myc cells compared with Rat1_vector cells.


title: Array CGH on gemcitabine resistant tumor

summary:
Biological material: One solid mouse tumor "Colon 26A" was routinely maintained by successive transplantation. A subset of mice with this tumor was treated at the maximum tolerable dosage of Gemcitabine and successively transplanted 5 times and similarly treated. The last passage was completly resistant and designated, "Colon 26G".

Oligo array CGH microarray: DNA from tumor and normal liver samples
were isolated using the Wizard Genomic DNA purification kit according to
the manufactures protocol (Promega Benelux BV, Leiden, NL). Labeling and
hybridization procedures for the oligo array CGH were performed as
previously described (Carvalho et al, 2004, J. Clin. Pathol., 57:644-649) with the following modifications: a mouse oligo library
version 2.0 (Compugen/Sigma-Aldrich Chemie B.V., Zwijndrecht, NL)
containing 21,997 oligonucleotides (65bp) representing 21,587 exon regions
on all chromosomes were spotted on the arrays. Prehybridisation was omitted
and Cot-1 concentrations during the hybridization were reduced to 100 µg.
Hybridizations were done using a Hybstation12 (Perkin-Elmer, Zaventem,
BE). CGH arrays were scanned using a laser scanner (Agilent Technologies,
Amstelveen, NL) and analyzed using Bluefuse Software v.2.0 (Bluegnome
Ltd, Cambridge, UK). Images show fused values; values with confidence
higher then 0.35 with the overall Cy3 and Cy5 channels normalized to a
log2ratio of 0. Tumor 26G
was hybridized twice and Bluefuse confidence based average values are
given. No further
normalizations were performed. For interpretation and visualization purposes,smoothing was performed by version 2 of aCGH smooth, with λ set to 2.0.
Keywords: other

first: Mark

last: van de Wiel

first: Jose

last: Costa

first: Kees

last: Smid

first: Cees

last: Oudejans

first: Andries

last: Bergman

first: Gerrit

last: Meijer

first: Godefridus

last: Peters


title: Arthritis and Rheumatism

status: Public on Dec 17 2005

last: Stanford Microarray Database

summary:
Synovial tissue mRNA from 21 RA patients and 9 OA patients is hybridized against a common reference sample on lymphochips.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Using regression correlation

first: Cornelis

last: Verweij


title: Intestine mRNA tagging

first: Florencia

last: Pauli

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

summary:
mRNA tagging in the intestine of C. elegans.  FLAG::PAB-1 was expressed from the intestine-specific promoter for ges-1 and used to immunoprecipitate FLAG::PAB-1/mRNA complexes from the intestine with anti-FLAG antibody on agarose beads.  This mRNA was amplified, cDNA was synthesized and labeled with Cy5.  Total RNA from the same strain, but without the IP was amplified and cDNA was synthesized and labeled with Cy3.  These two samples were compared on C. elegans DNA printed arrays from the Stuart Kim lab.  1938 intestine-expressed genes were identified (p<0.001) after eight repeats of the experiment
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.
Type = replicate_design
Series_overall_design: Computed
Keywords: other

first: Min

last: Jiang


title: Gene Expression Profiles of cutaneous B-cell lymphoma

summary:
We studied gene expression profiles of 17 cutaneous B-cell lymphomas that were collected with 4-6 millimeter skin punch biopsies. We also included tissue from 2 cases of mycosis fungoides (MF), 3 normal skin biopsies and 3 tonsils to create a framework for further interpretation. A hierarchical cluster algorithm was applied for data analysis. Our results indicate that small amounts of skin tissue can be used successfully to perform microarray analysis and result in distinct gene expression patterns. Duplicate specimens clustered together demonstrating a reproducible technique. Within the cutaneous B-cell lymphoma specimens two specific B-cell differentiation stage signatures of germinal center B-cells and plasma cells could be identified. Primary cutaneous follicular and primary cutaneous diffuse large B-cell lymphomas had a germinal center B-cell signature while a subset of marginal zone lymphomas demonstrated a plasma cell signature. Primary and secondary follicular B-cell lymphoma of the skin were closely related, despite previously reported genetic and phenotypic differences. In contrast primary and secondary cutaneous diffuse large B-cell lymphoma were less related to each other. This pilot study allows a first glance into the complex and unique microenvironment of B-cell lymphomas of the skin and provides a basis for future studies, that may lead to the identification of potential histologic and prognostic markers as well as therapeutic targets.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Monique

last: Vanoli-Storz


title: Rheumatoid arthritis and rheumatoid synovium

status: Public on Dec 15 2005

summary:
Rheumatoid arthritis (RA) is a heterogeneous disease. We used cDNA microarray technology to subclassify RA patients and disclose disease pathways in rheumatoid synovium. Hierarchical clustering of gene expression data identified two main groups of tissues (RA-I and RA-II). A total of 121 genes were significantly higher expressed in the RA-I tissues, whereas 39 genes were overexpressed in the RA-II tissues. Among the 121 genes overexpressed in RA-I tissues, a relative majority of nine genes are located on chromosome 6p21.3. An interpretation of biological processes that take place revealed that the gene expression profile in RA-I tissues is indicative for an adaptive immune response. The RA-II group showed expression of genes suggestive for fibroblast dedifferentiation. Within the RA-I group, two subgroups could be distinguished; the RA-Ia group showed predominantly immune-related gene activity, while the RA-Ib group showed an additional higher activity of genes indicative for the classical pathway of complement activation. All tissues except the RA-Ia subgroup showed elevated expression of genes involved in tissue remodeling. These results confirm the heterogeneous nature of RA and suggest the existence of distinct pathogenic mechanisms that contribute to RA. The differences in expression profiles provide opportunities to stratify patients based on molecular criteria.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs


title: Invasion by P. falciparum merozoites suggests a hierarchy of molecular interactions

city: Parkville

first: Ken

last: Simpson

state: Victoria

address: 1G Royal Parade

department: Genetics and Bioinformatics

country: Australia

institute: The Walter and Eliza Hall Institute

summary:
Central to the pathology of malaria disease are the repeated cycles of parasite invasion and destruction of human
erythrocytes. In Plasmodium falciparum, the most virulent species causing malaria, erythrocyte invasion involves
several specific receptor–ligand interactions that direct the pathway used to invade the host cell, with parasites
varying in their dependency on these different pathways. Gene disruption of a key invasion ligand in the 3D7 parasite
strain, the P. falciparum reticulocyte binding-like homolog 2b (PfRh2b), resulted in the parasite invading via a novel
pathway. Here, we show results that suggest the molecular basis for this novel pathway is not due to a molecular
switch but is instead mediated by the redeployment of machinery already present in the parent parasite but masked
by the dominant role of PfRh2b. This would suggest that interactions directing invasion are organized hierarchically,
where silencing of dominant invasion ligands reveal underlying alternative pathways. This provides wild parasites with
the ability to adapt to immune-mediated selection or polymorphism in erythrocyte receptors and has implications for
the use of invasion-related molecules in candidate vaccines.
Keywords: genetic modification

overall_design: 10 arrays, with some biological replication (3D7 wildtype x 2, PfRh2b knockout x2, D10 wildtype x 2).

first: Jake

last: Baum

first: Alexander

middle: G

last: Maier

first: Robert

middle: T

last: Good

first: Alan

last: Cowman


title: DNA microarray analysis of genes positively regulated by HapR

first: Melanie

last: Blokesch

department: Medical School

summary:
Vibrio cholerae strains A1552 and ATN140 (A1552-delta-hapR) were diluted 1:100 from over night cultures and grown aerobically (at 250 rpm) in M9 minimal medium supplemented with vitamins (MEM vitamin solution, BRL) and 0.5% lactate. At OD600 ~ 0.3 2 mM (GlcNAc)6 (Seikagaku America, East Falmouth, MA) was added and the cultures were further shaken for 2 hours. After harvesting the bacteria by centrifugation, the cell pellet was resuspended in Trizol reagent (GIBCO/BRL) and stored at -80 degrees C until further use. The procedure of RNA isolation and the corresponding amplicon microarray experiments was described by K. L. Meibom et al., Proc. Natl. Acad. Sci. U.S.A 101, 2524-9 (2004).
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Nadia

last: Dolganov

first: Karin

last: Meibom

first: Gary

last: Schoolnik


title: Sprague Dawley vs Ren-2

city: Melbourne

first: Maria

last: Schache

institute: St Vincents Institute

summary:
all data from control and diabetic
Keywords: other


title: Expression microarray analysis of acquired gemcitabine resistance

first: Daoud

last: Sie

summary:
This series repressents the data set from the paper "Expression microarray analysis and oligo array CGH of aquired gemcitabine resistance in mouse colon reveals selection for chromosomal aberrations".

Biological material: One solid mouse tumor "Colon 26A" was routinely maintained by successive transplantation. A subset of mice with this tumor was treated at the maximum tolerable dosage of Gemcitabine and successively transplanted 5 times and similarly treated. The last passage was completly resistant and designated, "Colon 26G".

Expression array: Total RNA was isolated from frozen mouse tumors using Tryzol. Single stranded cDNA was synthetized from 30 mg of total RNA by reverse transcription using aminoallyl labeled dUTP (Ambion). Labelling was performed according to the aminoallyl labeling protocol. Briefly, cDNA was incubated at room temperature for 1 h with fluorolink monofunctional cy5 or cy3 (Amersham) followed by 15 min 4 M hydroxylamine treatment. Uncoupled dyes were removed using Qiaquick PCR purification columns (Qiagen) and mixed with 12 mg poly(dA) (Amersham), 60 mg yeast tRNA (Sigma) and 24 mg Cot-1 DNA (Invitroen). The probe was dissolved in 127 ml hybridization mixture containing 46% formamide, 9.5% dextran sulfate, 2x SSC and 0.2% SDS. The probe was heated to 70°C for 10 min and annealed at 37°C for 1 h. Slides were hybridized for 14 h at 37°C over-night (HyArray 12™, Perkin Elmer). After hybridization the slides were washed in the HybArray 12™ with 50% formamide, 2x SSC, pH 7 at 35°C for 15 min, followed b PI buffer (0.1 M sodium phosphate, 0.1% Igepal Ca630, pH 8) at room temperature and 3 washes of 0.2x SSC, 0.1x SSC and 0.01x SSC at room temperature followed by centrifugation. Arrays were scanned using a laser scanner (ScanArray Express, Perkin Elmer) and analysed using ImaGene version 5.6. Cy5 cy3 ratios are calculating by taking the log2 of the signal mean of each spot minus the median background mean of all spots on the array. This is followed by a standard normalization for spot intensity and calculation of the ratios.
Keywords: other

first: Mark

middle: A

last: van de Wiel

first: Jose

last: Costa

first: Kees

last: Smid

first: Cees

last: Oudejans

first: Andries

last: Bergman

last: Meijer

first: Bauke

last: Ylstra


title: VP963/DK1622

status: Public on Dec 10 2005

city: Davis

first: Mitchell

last: Singer

address: 1 Shields Ave

department: Microbiology

institute: The University of California, Davis

summary:
Phosphate regulation is complex in the developmental prokaryote Myxococcus xanthus, and requires at least three previously characterized two-component systems (TCS), designated PhoR1-PhoP1, PhoR2-PhoP2, and PhoR3-PhoP3.  We report here the identification and characterization of a member of a fourth TCS, designated PhoP4, which shows high sequence similarity to the other three M. xanthus PhoP response regulators.  PhoP4 is an orphan response regulator that was identified by yeast 2-hybrid screen as a possible interacting partner of PhoR2.  phoP4 insertion mutation and in-frame deletion strains were constructed and assessed for developmental and phosphatase phenotypes, and then compared with the phenotypes previously reported for a _phoR2-phoP2 strain.  The data indicate that the phoP4 mutations caused spore viability to be decreased by nearly two orders of magnitude, and reduced all three development-specific phosphatase activities by 80-90% under phosphate-limiting conditions.  These phenotypes are stronger than those observed for mutations in the PhoR2-PhoP2 system, thereby suggesting a high degree of complexity vis-à-vis the interactions amongst the Pho signal transduction pathways in M. xanthus.
Keywords: developmental analysis

overall_design: 3 biological replicates with 3 time points each, normalized ratios to Cy3


title: Response of yeast cells to stress

last: Stanford Microarray Database

department: Stanford University, School of Medicine

summary:
Stress experiments repeating Gasch et al.,2000 conditions (Mol Biol Cell. 2000 Dec;11(12):4241-57). For each set of conditions I compared a deletion mutant for a predicted transcription regulator with a congenic wt strain.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Michael

last: Shapira


title: Identification of drug associated genes in ovarian cancer by RNA profiling

status: Public on Dec 11 2005

city: BOSTON

first: Kuan-Chun

last: Huang

state: MA

address: 221 Longwood Ave. BLI-431

department: OB-GYN

institute: Brigham and Women's Hospital

summary:
Two expression profilings were conducted in order to identify drug-associated genes in ovarian cancers. The first expression profiling was performed between RNAs from chemosensitive ovarian cancers and chemoresistant ovarian cancers. The second analysis was using a drug sensitive ovarian cancer cell line and a multi-drug resistant ovarian cancer cell line.
Keywords: other

first: Samuel

last: Mok

first: Shu-Wing

last: Ng


title: Chromosome-wide mapping of interactions of yeast nucleoporin Nup2 on chromosome VI.

status: Public on Dec 12 2005

city: Geneva 4

first: Ulrich

middle: K.

last: Laemmli

address: 30, quai Ernest-Ansermet

institute: University of Geneva

type: Genome binding/occupancy profiling by genome tiling array

summary:
This series is a complementary data set for the manuscript entitled "Nup-PI: The Nucleopore-Promoter Interactions of Genes in Yeast." (Mol. Cell, 2006).

Experimental Background:
Genomic interaction sites of nuclear proteins were mapped by the in vivo ChEC technique described in Schmid et al. (2004) Mol. Cell 16, 147-157. Genome-wide probes that are suitable for hybridization of microarrays were prepared. In brief, MboI restriction fragments that were internally cleaved by the MN moiety of the fusion proteins were amplified and labelled. The procedure is explained in detail in the manuscript. "Nup-PI: The Nucleopore-Promoter Interactions of Genes in Yeast." (Schmid et al., Mol. Cell 2006).

Experiments:
Genome-wide probes were prepared from control, uncleaved chromatin, as well as chromatin cleaved by H2b-MN and Nup2-MN. All samples were from raffinose grown cells induced for 1 hour by galactose in logarithmic growth phase.
Keywords: Genome-wide ChEC analysis, Mapping of Nuclear Pore Proteins

overall_design: 3 independent genome-wide probes were prepared for each Sample. That is, the ChEC experiments as well as preparation of genome-wide probes and hybridization of microarrays were carried independently (on different days). RMA values were calculated from the original .CEL files of each array and Average and standard deviation calculated.

first: Manfred

last: Schmid


title: Gene Expression Profiling of Ulcerative Colitis

status: Public on Dec 13 2005

city: Seoul

first: Inchul

last: Lee

address: 388-1 Poongnap-Dong, Songpa-Gu

country: South Korea

institute: University of Ulsan College of Medicine

summary:
Through laser capture microdissection and microarray analysis combined with slightly modified RNA extraction and amplification.   we could analyze the subtle differential expression between colon normal cell and ulcerative colitis.
Keywords: Ulcerative Colitis, amplification, microdissection

overall_design: GSM87318 is control sample and  GSM87319  is Ulcerative Colitis sample.

first: Iclee

first: Seunghyun

last: Bang


title: Effects of rraA overexpression on transcription

summary:
Effects of rraA overexpression on the global transcript profile of E. coli. This experiment set contains primary data for Figure 5A, Lee et. al. Cell 2003.
An RNA stablity experiment design type examines stability and/or decay of RNA transcripts.
Keywords: RNA_stability_design

first: Kangseok


title: Gene Expression Profiling Following DNA Vaccination of Rainbow Trout against Infectious Hematopoietic Necrosis Virus

status: Public on Dec 09 2005

city: West Lafayette

first: Krista

last: Nichols

state: IN

address: 915 W State Street

department: Biological Sciences

institute: Purdue University

summary:
The Infectious Hematopoietic Necrosic Virus (IHNV) DNA vaccine is based on the viral glycoprotein gene (G gene) and induces a non-specific anti-viral immune response and long-term specific immunity against IHNV in salmonid fishes. This study characterized gene expression responses associated with the early anti-viral response. Homozygous rainbow trout were injected intra-muscularly (I.M.) with vector DNA or the IHNV DNA vaccine. Gene expression at the I.M. site was evaluated using a 16,000 feature salmon cDNA microarray. Eighty different transcripts were significantly modulated in the vector DNA group while 910 transcripts were modulated in the IHNV DNA vaccinated group relative to control group. Quantitative reverse transcriptase PCR was used to examine expression of selected genes at the I.M. site and in other secondary tissues. In the localized response (I.M. site), the magnitudes of gene expression changes were higher in the vaccinate group relative to the vector DNA group for the majority of genes analyzed. At secondary systemic sites (e.g. gill, kidney and spleen) evaluated with RT-PCR of specific genes, the main difference was the up-regulation of the type I IFN-related genes in only the IHNV DNA vaccinated group.
Keywords: disease vaccine response

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Gene expression at the site of I.M injection was evaluated 7 days post-injection in clonal rainbow trout.  Gene expression was compared across three treatments, with replicate clonal rainbow trout individuals (Hot Creek strain) within each treatment.  Treatments included injection with 1X PBS (control group), plasmid vector only (without IHNV G gene; hereafter referred to as vector group), and the pIHNV vaccine (vaccine group).  Three clonal individuals from the control, three individuals from the vector group, and four individuals from the vaccine group were labeled with Cy3 and used for individual hybridizations to ten slides, comparing hybridization of each individual to a major reference RNA pool.  The major reference pool consisted of three unhandled clonal rainbow trout and constituted a pool of RNA from the anterior kidney, spleen, liver and muscle and was labelled with Cy5.  Total RNA was extracted from samples, amplified, and hybridized to 16,000 feature Atlantic salmon cDNA arrays developed by the Genomic Research for Atlantic Salmon project.  Differential expression was compared among control, vector, and vaccine groups.

first: Maureen

last: Purcell

first: Linda

last: Park

first: Gael

last: Kurath

first: Gary

last: Thorgaard

first: Paul

last: Wheeler

first: John

last: Hansen

first: Russell

last: Herwig

first: James

last: Winton


title: Gene expression in the duodenum of naive sheep genetically resistant and susceptible to gastrointestinal nematodes

status: Public on Dec 06 2005

city: Dunedin

first: Orla

middle: Mary

last: Keane

state: Otago

address: 710 Cumberland St

department: Animal Genomics

country: New Zealand

institute: AgResearch

summary:
This experiment compared gene expression in the duodenum of naive genetically resistant sheep and naive genetically susceptible sheep.
Keywords: resistant v susceptible

overall_design: A four factorial design was used with four resistant animals and four susceptible animals.  Each animal in the resistant group was compared to each animal in the susceptible group incorporating dye swaps.

first: Amonida

last: Zadissa

first: Theresa

last: Wilson

first: Dianne

middle: L

last: Hyndman

first: Gordon

middle: J

last: Greer

first: David

last: Baird

first: Alan

middle: F

last: McCulloch

first: Allan

last: Crawford

last: McEwan


status: Public on Dec 08 2005

city: Princeton

first: Alison

last: Hottes

state: NJ

address: 220 Carl Icahn Lab Washington Road

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary:
Supporting data for Chen et al., "Cytokinesis signals truncation of the PodJ polarity factor by a cell cycle-regulated protease"

The microarray component of this work seeks to identify genes whose expression is controlled by the Caulobacter crescentus DivJ-PleC-DivK system.
Keywords: time course, mutant/wild-type comparisons

overall_design:
We postulated that the DivJ-PleC-DivK system controls the expression of factors that regulate PodJ processing.  To identify such factors, we examined the transcriptional effects of the DivJ-PleC-DivK system using five perturbations.

1.  We compared expression between wild-type (CB15) and pleC deletion strains (LS3767, LS3768).  (4 arrays; all biological replicates; includes dye-swaps)

2.  We compared expression between wild-type (CB15) and strains with an allele of pleC in which amino acid 610 of the gene product was changed from a histidine to an alanine (LS3938, LS3939).  The H610A mutation abolishes both the kinase and phosphatase activities of PleC.  (5 arrays; all biological replicates; includes dye-swaps)

3.  We compared expression between wild-type (CB15) and strains with a divJ deletion (LS4107, LS4108) or disruption (LS4110, LS4117).  Two different divJ null alleles, each with a different antibiotic resistance gene cassette, were used to reduce the impact that the antibiotic resistance genes might have on the analysis.  (Cells were grown without antibiotics.)  (4 arrays; all biological replicates; includes dye swaps)

4.  We compared expression between wild-type (CB15) and a podJ deletion strain (LS3766).  PodJ is required for the normal localization of PleC.  (4 arrays; all biological replicates; includes dye-swaps)

5.  We monitored expression during the cell cycle in a synchronized population of cells carrying the cold-sensitive divKD90G allele.  Samples were taken throughout the cell cycle and each sample was compared to a common reference.  (22 arrays; 14 time points, of which 8 contain technical replicates)

first: Joseph

last: Chen

first: Harley

last: McAdams

first: Patrick

last: McGrath

last: Viollier

first: Lucy

last: Shapiro


title: Gene Expression Profiling in Prostate Cancer Cells With Akt Activation

status: Public on Dec 03 2005

last: Stanford Microarray Database

state: CA

summary:
To determine which genes may be regulated by Akt and participate in the transformation of cells, we have examined by microarray analyses genes turned on in the prostate cancer cell line, PC3, when Akt activity was induced. PC3 cells, which lack the lipid phosphatase PTEN, were treated overnight with a reversible inhibitor of the phosphatidylinositol 3-kinase, LY294002 (a treatment which was found to reversibly decrease Akt enzymatic activity). The inhibitor was then washed out and mRNA collected 2, 6, and 10 h later and compared by microarray analyses with mRNAs present immediately after removal of the inhibitor. One of the identified induced mRNAs, Fra-1, was further studied by transient transfections of a reporter construct containing its 5' regulatory region. This construct was found to be directly induced 4- to 5-fold by co-transfection with constitutively active Akt3 but not kinase dead Akt. The regulation by Akt3 was found to be due to two specific regions in the Fra-1 regulatory sequence which match Sp1 consensus sites. Finally, gel shift studies showed that the binding of Sp1 to one of these sites was dependent on the PI 3-kinase pathway. These results indicate that LY294002 treatment and washout is a useful method to study the activation of Akt in the context of a tumor cell. Moreover, the identification of Fra-1 as an Akt-regulated gene may have implications for the ability of Akt to transform cells since Fra-1 has been implicated in cell growth and the aggressiveness of tumors.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Jonathan

last: Pollack


title: Neurosphere SAGE library

first: Theodore

last: Perkins

summary:
Putative neural stem cells were derived from E12-E14 stiatal tissue and that was cultured for 10-12 dy s in neural stem cell media supplemented with bFGF
Keywords: other

overall_design: this experiment include 1 samples and 1 replicates


title: HTC avian macrophage cells stimulated with 3 species of Eimeria across a 48 hour timecourse

city: Newark

first: Calvin

last: Keeler

state: DE

department: Animal and Food Sciences

institute: University of Delaware

summary:
HTC avain macrophage cell line was stimulated with E. tenella, acervulina, and maxima for 0, 4, 18, and 48 hours.  Total RNA was extracted, mRNA was purified, and RNA samples were directly labeled with Alexa555 or 647.  The experiment was performed in loop format, so that each sample was labeled with both dyes and hybridized to two different slides.  Images were acquired by the Applied Precision ArrayWoRx scanner and software and then intensity values were obtained using Softworx Tracker.
Keywords: timecurse, species comparison

overall_design: The experiment was performed in loop format, so that each sample was labeled with both dyes and hybridized to two different slides.  Since there were 4 samples per species and 3 speies, there were 12 total samples.  Each sample was labeled with both dyes, so there were 24 separate labelings and 12 slides hybridized.

first: Rami

last: Dalloul

first: Travis

middle: W

last: Bliss

first: Hyun

last: Lillehoj


title: Acid exposure

summary:
Two independent exposures (labeled T1 and T2) to pH 5.0.  Samples were harvested at 30, 60, 90 and 120 minutes and used to make cDNA.  Arrays are set up such that each time point was hybridized to the individual T=0 starting culture.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: DS

last: Merrell


title: Genome-wide transcriptional profiling of Lactobacillus acidophilus stress response

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

state: NC

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

summary:
We used a whole genome array containing 97.4 % of the annotated genes of Lactobacillus acidophilus NCFM, a probiotic culture that belongs to the lactic acid bacteria group, to identify genes that are differentially expressed under several stress conditions.
Keywords: Stress response

overall_design: We used a Reference Sample design, where each sample was compared using a dye swap to a common reference sample (early log-phase L. acidophilus cultures resuspended in fresh MRS [pH ~6.8]).

first: Maria

last: Azcarate-Peril

middle: R


title: Dipyridyl Treatment

summary:
Culture was split into halves and 500 uM dipyridyl was added to one half.  Samples were collected after the indicated times.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

first: Charlie

last: Kim


title: Genetic instability in colon cancer

address: 269 Campus Drive, CCSR3245A

summary:
Experimental set accompanying Giacomini et al publication "A legacy gene-expression signature of genetic instability in colon cancer".  Includes 18 colon cancer cell line training set, 13 colon cancer cell line test set, and 3 cell lines (HCT116, HCT116+ch2, HCT116+ch3) used to evaluate signature after correcting underlying genetic instability.  Experiments were performed by comparing mRNA from each colon cancer cell line (Cy5; channel 2) to a "universal" mRNA reference (Cy3; channel 1).
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Series type: disease_state_design
Series_overall_design: Using regression correlation
Keywords: other

first: Craig

last: Giacomini


last: Hottes

summary:
Supporting data for Hottes et al., "DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus"

The microarray component of this work monitors mRNA expression during the cell cycle of synchronized populations of Caulobacter crescentus cells.  Transcription during the normal cell cycle is compared with transcription during a cell cycle where expression of dnaA, which encodes a key DNA replication initiation factor, is delayed.
Keywords: time course, cell cycle, metabolism

overall_design:
1.  Using a synchronized population of CB15N cells, we monitored expression during the cell cycle in cells grown in M2G media. Samples were taken throughout the cell cycle and each sample was compared to a common reference. (22 arrays; 11 time points each of which has a technical replicate)

2.  Using a synchronized population of CB15N cells, we monitored expression during the cell cycle in cells grown in PYE media. Samples were taken throughout the cell cycle and each sample was compared to a common reference. (14 arrays; 11 time points of which 3 have a technical replicate)

3.  We monitered mRNA expression during a cell cycle where expression of dnaA, which encodes a replication initiation factor, was delayed.  We used a strain where the only copy of dnaA was on the chromosome under the control of an inducible promoter.  First, we isolated swarmer-stage cells from a culture grown in conditions where dnaA was expressed.  Then, the swarmer cells were released into conditions where dnaA was not expressed.  The cells blocked in the G1-stage.  Later, expression of dnaA was turned on, causing the cells to initiate DNA replication and finish the cell cycle.  Samples were taken throughout the cell cycle and each sample was compared to a common reference. (21 arrays; 15 time points of which 6 have a technical replicate)

4.  We repeated the experiment described in 3 with a different culture of cells (22 arrays, 14 timepoints of which 8 have technical replicate)

5.  In 3 and 4 (above) we controlled dnaA expression using a xylose-inducible promoter.  To identify genes whose expression is sensitive to xylose, we compared expression of asynchronous populations of CB15N grown on M2G (minimal media with glucose as the sole carbon source) to asynchronous populations of CB15N grown on M2GX (minimal media with glucose and xylose as carbon sources).  (4 arrays, all biological replicates)


title: DNA microarray analysis of genes positively regulated by TfoX

first: Melanie

last: Blokesch

summary:
Vibrio cholerae strains A1552tfoX/pBAD and A1552tfoX/pBAD-tfoX were diluted 1:100 from over night cultures and grown in LB liquid medium containing 0.2 % L-arabinose and 100 μg/ml ampicillin. At OD600=0.3, samples were quickly harvested in a microcentrifuge at room temperature and the bacterial pellet resuspended in Trizol reagent (GIBCO/BRL) and kept at -80 degrees C. The aqueous phase containing the RNA was isolated according to the manufacturer's manual and to which was added an equal volume of 70% ethanol. Using an RNeasy. column (Qiagen, Valencia, CA) the RNA was isolated and treated with DNase I solution. Labeling of cDNA was done as described by M. I. Voskuil et al., J. Exp. Med. 198, 705-13 (2003). Samples from A1552tfoX/pBAD were labeled with Cy3 and samples from A1552tfoX/pBAD-tfoX were labeled with Cy5. Duplicate samples from two individual experiments were hybridized to an oligonucleotide DNA microarray slide containing at least one oligonucleotide corresponding to every identified open-reading-frame of V. cholerae O1 El Tor strain N16961. Microarray slides were prehybridized (5 x SSC, 1% BSA, 0.1% SDS) for at least one hour at 42 degrees C and hybridization was performed in 2 x SSC, 0.1% SDS, 20% formamide at 54 degrees C over night.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Karin

last: Meibom

first: Nadia

last: Dolganov

first: Gary

last: Schoolnik


title: Switch from LB pH7 to M9 pH5

last: Stanford Microarray Database

summary:
Salmonella must express and deploy a type III secretion system located in Salmonella pathogenicity island 2 (SPI-2) in order to survive in host phagocytic vacuoles and to cause systemic infection in mouse models of typhoid fever. A genome-wide approach to screening for Salmonella genes that are transcriptionally co-regulated in vitro with SPI-2 genes was used to identify bacterial loci that might function in a mouse model of systemic disease. Strains with mutations in three SPI-2 co-expressed genes were constructed and tested for their ability to cause disease in mice. We found that virK, a homologue of a Shigella virulence determinant, and rcsC, a sensor kinase, are important at late stages of infection. A second Salmonella gene that has VirK homology, somA, is also important for systemic infection in mice. We have shown that expression of both virK and somA requires the transcription factor PhoP, whereas rcsC does not. Additionally, rcsC expression does not require the transcription factor OmpR, but expression of one of the known targets of RcsC, the yojN rcsB putative operon, does require OmpR. virK, somA and rcsC are expressed in tissue culture macrophages and confer Salmonella resistance to the cationic peptide polymyxin B. We conclude that virK, somA and rcsC are important for late stages of Salmonella enteric fever, and that they probably contribute to the remodelling of the bacterial outer membrane in response to the host environment.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

first: Nina

last: Salama


title: Yeast translation

summary:
Red channel: 3 independent polysome preparations from BY4741 cells, grown in YPD to mid-log phase (OD 0.6-0.9). In each experiment 14 fractions were collected. In-vitro transcribed B.subtilis controls were added to each fraction and used for normalization. Green channel: Total RNA prepared from S288c cells.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Yoav

last: Arava


title: Arabidopsis microarrays identify conserved and differentially-expressed genes involved in shoot grow

summary:
Expressed sequence tags (EST)-based microarrays are powerful tools for gene discovery and signal transduction studies in a small number of well-characterized species. To explore the usefulness of this technique for poorly characterized species, we have hybridized the 11 522-element Arabidopsis microarrays with labeled cDNAs from mature leaf and shoot apices from several different species. Expression of 23 to 47% of the genes on the array was detected, demonstrating that a large number of genes from distantly related species can be surveyed on Arabidopsis arrays. Differential expression of genes with known functions was indicative of the physiological state of the tissues tested. Genes involved in cell division, stress responses, and development were conserved and expressed preferentially in growing shoots.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: David

last: Horvath