title: Halibut Developmental Series

status: Public on Feb 10 2008

city: Halifax

first: Jason

last: Williams

state: Nova Scotia

address: 1411 Oxford Street

department: Institute for Marine Biosciences

institute: National Research Council

summary:
 An oligonucleotide microarray containing 50-mer oligonucleotides representing 9277 unique Atlantic halibut genes has been designed, printed and is currently being used for the study of gene expression in developing halibut.  The oligonucleotides are based on all of the Atlantic halibut data available at the time of printing; these included ESTs and complete cDNAs derived from the Pleurogene sequencing project as well as sequences deposited in GenBank by other groups as of September 2006. Of the Pleurogene ESTs, 5040 are functionally annotated; the remainder are unknown (1016) or are similar to unannotated sequences in GenBank (1626).  In addition to Atlantic halibut features, several control features have been incorporated, including an oligonucleotide representing a heterologous plant gene (92 spots) and empty spots containing buffer only (1344). The array contains 48 subgrids, each comprised of 32 columns and 26 rows. Every feature is printed at least four times as side-by-side quadruplicates, resulting in a microarray containing 39936 features. This microarray has been utilized to identify genes differentially expressed in larval Atlantic halibut during the developmental period from post-hatch to post-metamorphosis.
Keywords: Development stage comparison

overall_design:
Two colour design. Oligonucleotide DNA probes were designed from approximately 13000 available Atlantic halibut ESTs.  The majority of the ESTs were derived by sequencing from the 5’ end of clones from 13 different normalized libraries from eight different tissues and five different developmental stages (Douglas et al., 2007). All EST data have been deposited in GenBank (accession numbers EB029285-EB041700 & EB080851-EB080975), and preliminary annotations are available on the Pleurogene website (www.pleurogene.ca).  Additional unique ESTs from other research groups that were present in GenBank were also used.  Oligonucleotide probes wFere designed using ArrayDesigner software (Premierbiosoft, Palo Alto, CA, USA). Probe sequences were selected to have minimal secondary structure, a GC ratio between 40-60%, a melt temperature of 75 ± 5oC and to be 45-55-mer in length. Uniqueness of the selected probes was ensured by BLAST comparison against all of the ESTs and the zebrafish genome.

Halibut DNA probes were synthesized at the Atlantic Microarray Facility (Moncton, NB, Canada) by the phosphoramidite method at a 40 nmole scale on a Gene Machines PolyPlex 2 oligonucleotide synthesizer (Genomic Soutions, Ann Arbor, MI, USA). Isolated DNA was analyzed by Electrospray ionisation-Mass Spectrometry using an Agilent VL1100MSD mass spectrometer (Agilent Technologies, Inc., Mississauga, ON, Canada). DNA of low quality was re-synthesized. In addition to the halibut probes, 1344 control spots containing buffer only, and 92 control spots containing an oligonucleotide specific to the chlorophyll synthetase G4 from Arabidopsis thaliana (GenBank Acc. U19382) were included.   Solutions (20 uM) in sodium phosphate Schott-Nexterion Spot buffer (Schott, Jena, Germany) were prepared in 384-well plates (Genetix X7020) and spotted in quadruplicate on epoxide microarray slides (Schott) to give 39936-feature microarrays. An OmniGrid 100 microarrayer (Genomic Solutions) equipped with SMT-S50 silicon print pins (Parallel Synthesis Technology, Santa Clara, CA, USA) was used.

Spotted microarrays were analyzed by SpotQC (IDT Inc., Coralville, IA, USA) for any defects in spotting that may have occurred. Microarrays were stored at room temperature in vacuum-sealed microarray pouches (Corning Inc., Corning, NY, USA).

Larval Sampling

Larvae were sampled at five different stages: hatching (1 dph; 10 mm), mouth opening (21 dph;15 mm), midway to metamorphosis (64 dph; 20 mm), premetamorphosis (91 dph; 25 mm), and post-metamorphosis (104 dph; 30-35 mm).  Three biological replicates were sampled at each stage.  Larval samples were pooled as follows: ~20 larvae each for post-hatch stage and 5 larvae each for all of the later developmental stages.

RNA Isolation

RNA was extracted from three biological replicates of pooled larvae at each of the five stages using the RNeasy Plus Mini kit (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s protocol. RNA quality was assessed using a Bioanalyser 2100 (Agilent Technologies, Inc.) and RNA was only used if the RIN value was at least 8.0.  A universal RNA reference sample was prepared that consisted of equal amounts of RNA from all 15 RNA preparations.

cDNA Preparation and Labeling

RNA (7.5 ug) from universal RNA reference and experimental samples was reverse transcribed and labeled using the SuperscriptTM Plus Direct cDNA labeling system (Invitrogen, Carlsbad, CA, USA) with Alexa 555 (experimental) and Alexa 647 (reference) fluorophores. An 8 ng spike of Arabidopsis chlorophyll synthetase G4 transcript was also included in the reverse transcription reaction as in internal control.  Labeled targets were hydrolyzed and purified using the QIAquick PCR purification kit (Qiagen). Purified labeled targets were quantitated using a NanoDrop® ND-1000 spectrophotometer (NanoDrop® Technologies Inc., Wilmington, DE, USA) and used if cDNA yield was greater than 20 ng/uL and fluorophore incorporation was at least 1.5 pmol/uL. Labeled targets (20 ul each of control and experimental samples) were mixed with 20 uL DIG EasyHyb buffer (Roche Applied Science, Laval, PQ, Canada), denatured at 95 oC for 3 min, centrifuged briefly, and hybridized to the microarrays.

Hybridization to Microarray

Slides were blocked in 100 mL of Nexterion Block E (Schott) at 50 oC for 1 h.  They were rinsed in 100 ml dH2O for 1 min at room temperature and dried by centrifuging at 200 x g for 5 min. Lifter Slip cover slips (Erie Scientific, Portsmouth, NH, USA) were washed in dH2O and 95% ethanol, wiped dry, and gently placed over the microarray.  Hybridzsation buffer containing the labeled targets (60 uL) was carefully applied to one corner of the Lifter Slip and immediately placed in the hybridization chamber (Die Tech, San Jose, CA, USA) to prevent drying. A small volume (60 uL) of hybridization buffer was added to wells in the bottom of the hybridization chamber to maintain moisture content, the chamber was closed, and incubated overnight at 30 oC in a water bath. Microarrays were washed once for 10 min at room temperature in 2X SSC with 0.2% SDS, twice for 10 min each at room temperature in 0.1X SSC, and dried by centrifugation at 200 x g for 5 min.

Scanning and Data Analysis

Microarrays were scanned at 543 and 633 nm using a ScanArray® 5000XL Microarray Acquisition scanner (Packard Bioscience, Billerica, MA, USA) at a resolution of 10 um. Laser power was set at levels between 80 and 100% and photomultiplier tube settings were set at values ranging from 70 to 95% to adjust Alexa555 and Alexa647 channels on individual slides.  Spot intensities were measured using ScanArray® Express (version 3.0.1.0001) microarray analysis software (Perkin Elmer LAS, Waltham, MA, USA), and the CSV files loaded into the ArrayPipe (Hokamp et al., 2004) server at the Institute for Marine Biosciences. Appropriate labels for common reference and treatment were set as follows: Channel1 for all slides was annotated as ‘C’ (common reference), and Channel2 was annotated as T1 through T5, with T1 corresponding to samples from post-hatch and T5 corresponding to samples from post-metamorphosis. Processing steps in Arraypipe consisted of ‘Flagging Markers’ (control features labeled as ‘buffer only’ and ‘Arabidopsis’) for exclusion from further analysis; background correction using the ‘limma normexp’ module with an offset of 50; subgrid (print-tip) normalization via the ‘limma loess’ (Smyth and Speed, 2003) module with span = 0.3, bin = 0.01,  and iterations = 4. Replicate features (4 replicates for each feature) were merged by computing the median value of all unflagged replicates. In all operations, features flagged by ScanArray® Express were excluded.

Spot ratios between pairs of successive developmental stages were compared individually using significance analysis of microarrays (SAM) (Tusher et al., 2001). To enable comparison of ratios between successive developmental stages, the output files for each slide were downloaded from Arraypipe, and the normalized, merged log2 ratios for each stage were input to the SAM Excel module. Genes used in SAM were unflagged in all replicates for both developmental stages being compared. In each comparison, the first developmental stage was labeled ‘1’, and the second ‘2’. The SAM mode was ‘two class unpaired’, using a t-test with 100 permutations.

For principal components analysis (PCA), the background-corrected, normalized, merged log2 ratios from ArrayPipe were imported into Matlab®. The data set was truncated to contain only those ratios that were unflagged across all 15 slides, resulting in a data matrix of 588 rows (features) by 15 columns (slides). Each column of the data matrix was mean centered, and analyzed by PCA via singular value decomposition (SVD) (Anderson et al., 1999). In this work, only the scores of the first two principal components (PCs) were examined.

first: Susan

middle: E

last: Douglas


title: cDNA aCGH study of whole genome amlification effect on analysis of FFPE microdissected human breast cancer

city: Toronto

last: Done

address: 610 University Ave

country: Canada

institute: Ontario Cancer Institute

summary:
6 samples of FFPE breast cancer tissue, whole genome amplification methods tested for fidelity: 3 samples amplified by two techniques (SCOMP and DOP) and compaed to non amplified control, 3 samples amplified additionally by the better performing technique (SCOMP)
Keywords: Pre-clinical method validation, whole genome amplification for use with aCGH

overall_design: Histological sections microdissected, DNA extracted, subjected to whole genome amplification protocol and aCGH.

first: Vladimir

last: Iakovlev


title: Gene expression profile in individuals affected by Mucolipidosis type IV

status: Public on Feb 11 2008

city: brescia

first: andrea

last: bozzato

address: viale europa 11

country: Italy

institute: university of brescia

summary:
We compared gene expression profiling of fibroblasts from individuals affected by Mucolipidosis type IV (MLIV) and healthy ones (AB).
Keywords: Disease state analysis

overall_design: We directly compared MLIV indivisuals versus normal controls. A total of four technical replicate hybridizations were performed.


title: MCF-7_HRG_transcript_mapping

status: Public on Feb 08 2008

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

type: Expression profiling by genome tiling array

summary:
Heregulin beta-1 (HRG) is an extracellular ligand that activates mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-OH kinase (PI3K)/Akt signaling pathways through ErbB receptors. MAPK and Akt have been shown to phosphorylate the estrogen receptor (ER) at Ser-118 and Ser-167, respectively, thereby mimicking the effects of estrogenic activity such as estrogen responsive element (ERE)-dependent transcription. In the current study, integrative analysis was performed using two tiling array platforms, comprising histone H3 lysine 9 (H3K9) acetylation and RNA mapping, together with  array comparative genomic hybridization (CGH) analysis in an effort to identify HRG-regulated genes in ER-positive MCF-7 breast cancer cells. Through application of various threshold settings, 333 (326 up-regulated and 7 down-regulated) HRG-regulated genes were detected. Prediction of upstream transcription factors (TFs) and pathway analysis indicated that 21% of HRG-induced gene regulation may be controlled by the MAPK cascade, while only 0.6% of the gene expression is controlled by ERE. A comparison with previously reported estrogen (E2)-regulated gene expression data revealed that only 12 common genes were identified between the 333 HRG-regulated (3.6%) and 239 E2-regulated (5.0%) gene groups. However, with respect to enriched upstream TFs, 4 common TFs were identified in the 14 HRG-regulated (28.6%) and 13 E2-regulated (30.8%) gene groups. These results indicated that while E2 and HRG may induce common TFs, the regulatory mechanisms that govern HRG- and E2-induced gene expression differ.
Keywords: time course, dose response, transcript mapping

overall_design: MCF-7 human breast cancer cells were incubated 2hr after administration of  heregulin (HRG). Control was set as growth hormone non-treated cells.


title: A linear-mixed model approach to identify expressed SFPs using short oligo microarrays - Placenta vs. Fibroblast

status: Public on Feb 09 2008

city: Raleigh

first: Nicholas

middle: Eldon

last: Hardison

state: NC

address: 4700 Hillsborough St., Room 318A

country: USA

institute: North Carolina State University

summary:
Background: Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed with Affymetrix porcine microarrays is presented. A linear mixed model analysis was used to identify significant breed-by-probe interactions.  This dataset uses different tissue types to explore the consequences of additional sample variance.
Keywords: Transcriptional profiling of porcine tissues

overall_design: 6 samples: 3 Day 30 occidental fibroblast, 3 Day 25 Meishan placenta.

first: Steve

middle: R

last: Bischoff

first: Shengdar

last: Tsai

first: Brad

middle: A

last: Freking

first: Dan

last: Nonneman

first: Gary

last: Rohrer

first: Jorge

last: Piedrahita


title: RNAi expression experiments on Illumina BeadChip

city: Urbana

first: jun

last: cai

state: IL

address: Springfield Ave, DCL

institute: UIUC

summary:
Mouse embryonic stem cells (mES) were depleted of Klf2, Klf4, and Klf5 by ectopic expression of shRNA. Control RNAi was performed using shRNA against luciferase. At 2 days, 4 days and 6 days post-transfection of shRNA-encoding vectors, cells are harvested for RNA isolation.
Keywords: RNAi expression, Mouse ES cells

overall_design: Knockdown: Klf2, Klf4, Klf5, Luciferase (Control);Time: 2 days post-transfection, 4 days post-transfection, 6 days post-transfection;Three independent experimental replicates for each experimental condition were  performed.

first: Huck

middle: H

last: Ng


title: ChIP-chip on custom NimbleGen genomic tiling arrays

type: Genome binding/occupancy profiling by genome tiling array

summary:
Performing Chromatin IP of Klf2, Klf4, Klf5 and p53 in mouse embryonic stem cells with NimbleGen custom genomic tiling arrays, we sought to decipher Klf2, Klf4, Klf5-regulated genes.
Keywords: genomic tiling arrays, ES cells

overall_design: 12 samples: Chromatin IP of Klf2, Klf4, Klf5 and p53 in mouse embryonic stem cells with NimbleGen custom genomic tiling arrays; three independent experimental replicates for each experimental condition were  performed.


title: Transcriptional profiling of Arabidopsis thaliana grown under arsenate stress

city: Knoxville

last: Abercrombie

state: TN

address: 2431 Joe Johnson Blvd.

department: Plant Sciences

institute: University of Tennessee

summary:
We examined the changes in gene expression in Arabidopsis thaliana grown under arsenate stress.  The transcriptional profiling reveals antioxidant activity and repression of the phosphate starvation response.
Keywords: dual label, stress response

overall_design: This experiment included a comparison of three biological replicate controls against three biological arsenate-stressed replicates with a dye-swap technical replicate for a total of six microarray slide hybridizations.

first: Matthew

last: Halfhill

first: Priya

last: Ranjan

first: Murali

last: Rao

first: Arnold

last: Saxton

first: Joshua

last: Yuan

first: C

middle: N

last: Stewart Jr.


title: Pharmacogenomic Approach for the Identification of Novel Determinants of Resistance to Oxaliplatin in Colon Cancer

status: Public on Feb 07 2008

city: Pamplona

first: Eva

last: Bandres

address: Avda Pio XII, 55

department: Cancer Research Program

country: Spain

institute: Center for Applied Medical Research (CIMA), University of Navarra

summary:
Oxaliplatin is a member of the family of Pt-containing chemotherapeutic agents that also include cisplatin (CDDP) and carboplatin. OXA is distinguished from these two older drugs by its different spectrum of activity both in preclinical models and in clinical trials. It is the only platinum analogue to have activity in colon cancer, a disease for which this drug has now become a mainstay of therapy. It mainly forms intrastrand adducts between two adjacent guanine residues or guanine and adenine, disrupting DNA replication and transcription. OXA has been reported to be involved in the Nucleotide Excision Repair Pathway (NER), p38 kinase activation, PI3K/AKT pathway and caspases cascade activation through apoptotic intrinsic pathway. However, the downstream molecular events underlying the cytotoxic effects of this chemotherapeutic agent have not been well characterized. This study was developed in order to clarify the multifactoriality of the resistance acquisition process and to identify genes and pathways that could play a role as markers in OXA sensitivity.
Keywords: Drug resistance

overall_design: The goal of our experiment was to determine a gene expression profile that discriminates between the OXA-sensitive colorectal cancer cell lines HT29, LoVo, DLD1 and LS513 group and the group of OXA-resistant derived cell lines HTOXAR3, LoVOXAR3, DLDOXAR3 and LSOXAR3 in order to clarify the multifactoriality of the resistance acquisition process and to identify genes and pathways that could play a role as markers in OXA sensitivity. The experimental design used was “RNA-Reference” and “Dye-Swap”. Each cell line was analyzed in duplicate, with RNA reference (Stratagene) as reference sample and labeled each biological condition once by Cy3 and once by Cy5. Taking the average of two arrays thus labeled, cancel the dye effect on any particular gene. In total we used 16 slides.

first: Martinez-Cardús

last: Anna

first: Martinez-Balibrea

last: Eva

first: Bandres

first: Malumbres

last: Raquel

first: Taron

last: Miquel

first: García-Foncillas

last: Jesus

first: Abad

last: Albert


title: MCF-7_HRG_H3K9Ac_ChIP-chip

first: Takahiro

last: Suzuki

summary:
Heregulin beta-1 (HRG) is an extracellular ligand that activates mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-OH kinase (PI3K)/Akt signaling pathways through ErbB receptors. MAPK and Akt have been shown to phosphorylate the estrogen receptor (ER) at Ser-118 and Ser-167, respectively, thereby mimicking the effects of estrogenic activity such as estrogen responsive element (ERE)-dependent transcription. In the current study, integrative analysis was performed using two tiling array platforms, comprising histone H3 lysine 9 (H3K9) acetylation and RNA mapping, together with  array comparative genomic hybridization (CGH) analysis in an effort to identify HRG-regulated genes in ER-positive MCF-7 breast cancer cells. Through application of various threshold settings, 333 (326 up-regulated and 7 down-regulated) HRG-regulated genes were detected. Prediction of upstream transcription factors (TFs) and pathway analysis indicated that 21% of HRG-induced gene regulation may be controlled by the MAPK cascade, while only 0.6% of the gene expression is controlled by ERE. A comparison with previously reported estrogen (E2)-regulated gene expression data revealed that only 12 common genes were identified between the 333 HRG-regulated (3.6%) and 239 E2-regulated (5.0%) gene groups. However, with respect to enriched upstream TFs, 4 common TFs were identified in the 14 HRG-regulated (28.6%) and 13 E2-regulated (30.8%) gene groups. These results indicated that while E2 and HRG may induce common TFs, the regulatory mechanisms that govern HRG- and E2-induced gene expression differ.
Keywords: time course, dose response, ChIP-chip


title: Inflammatory response of trout head kidney to in vivo challenge with IHN virus and LPS

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary:
The response of the trout, O.mykiss, head kidney to bacterial lipopolysaccharide (LPS) or active and attenuated infectious hematopoietic necrosis virus (IHNV and attINHV respectively) intraperoniteal challenge, 24 and 72 hours post-injection, was investigated using a salmonid-specific cDNA microarray. The head kidney response to i.p. LPS-induced inflammation in the first instance displays an initial stress reaction involving suppression of major cellular processes, including immune function, followed by a proliferative hematopoietic-type/biogenesis response 3 days after administration. The viral response at the early stage of infection highlights a suppression of hematopoietic and protein biosynthetic function and a stimulation of immune response. In fish infected with IHNV a loss of cellular function including signal transduction, cell cycle and transcriptional activity 72 hours after infection reflects the tissue-specific pathology of IHNV infection. attIHNV treatment on the other hand shows a similar pattern to native IHNV infection at 24 hours however at 72hours a divergence from the viral response is seen and replace with a recovery response more similar to that observed for LPS is observed.
Keywords: Viral and LPS transcriptomic response, IHNV, Trout

overall_design:
Rainbow  trout, Oncorhynchus mykiss  were intraperitoneally injected with saline (control) and LPS (6mg/Kg), or with 100 μl of a 106 pfu/ml dilution of IHNV or attIHNV or culture medium (negative control). At defined time points, 24 and 72 hours post i.p. injection, animals (total n=6), control and experimental, were selected from each  tank  (n=2) and  sacrificed. Head kidneys (HK) were immediately dissected out, pooled and processed for total RNA purification using  Tri  Reagent  (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer’s protocol.The design of the microarray includes 1380 genes printed  in  six  replicates each. Random clones  from common and subtracted  cDNA  libraries  (976)  were  compared  with  the  known  vertebrate  proteins using blastx and 686 genes were identified; the functional annotations were transferred from  the putative homologs. These clones were supplemented with 297 genes selected by the categories of Gene Ontology. Overall, each microarray was enriched in a number of  functional  classes,  such  as  stress  and  defense  response  (145  and  105  genes, respectively), cell cycle (62 genes), signal transduction (114 genes), chaperone activity (41 genes), and apoptosis (79 genes).  Total RNA obtained from head kidney tissue was verified for quantity and integrity by denaturing  electrophoresis  and  labeling  with  Cy3-  and  Cy5-dCTP  (Amersham
Pharmacia) was completed using SuperScript  III  reverse  transcriptase  (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore). We used a dye swap experimental design and each sample was hybridized to two microarrays. For the first slide, test and control cDNA were labeled with Cy5 and Cy3 respectively, and for  the  second array dye assignment was  reversed. All head  kidney  samples were analyses  using  the  dye  swap  protocol.  Scanning was performed with ScanArray 5000 and  images were processed  with  QuantArray  (GSI  Luminomics. After  subtraction  of mean background, locally weighted non-linear  regression (Lowess) normalization was performed separately for each slide. To assess differential expression of genes, the normalized  log  intensity  ratios  were  analyzed  with  Student’s  t-test  (p<0.01).  The Bayesian modification to the false discovery rate (FDR) was used to correct for multiple comparison  tests,  estimating  the  q-value  for  the  set  of  differentially  expressed  genes

first: Simon

last: Mackenzie

first: Juan

middle: C

last: Balasch

first: Beatriz

last: Novoa

first: Laia

last: Ribas

first: Nerea

last: Roher

first: Antonio

last: Figueras


title: Drought stress: Analysis of FDH (Formate dehydrogenase) insertion mutants in response to drought stress

status: Public on Feb 13 2008

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary:
adt04-03_fdh_drought - drought stress - What is the role of the mitochondrial formate dehydrogenase in the response to drought?								 - Wild type and mutant arabidopsis plants were grown in soil for 6 weeks under short days. Each lot of plants is shared into 2 groups, one of which was watered normally (arr) whislt the other half was not watered for a week (sech).
Keywords: gene knock out,treated vs untreated comparison

overall_design: 7 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

middle: P

last: Renou

first: Catherine-

last: Colas des Francs-Small

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Gene expression patterns within cell lines are predictive of chemosensitivity

city: Burlingame

first: Douglas

last: Ross

state: CA

address: 863 Mitten Rd #103

institute: Applied-Genomics

summary:
We generated RNA's and measured expression of 40000 genes using spotted cDNA microarrays from the fifty nine publicly available cell lines of the NCI Developmental Therapeutics Program's NCI60 studies and an additional set of seven cell lines for which GI50 compound sensitivity data were available. All cell lines were grown to 80% confluence in RPMI 1640 supplemented with phenol red, glutamine (2 mM) and 5% fetal calf serum. This expression data, in conjunction with the compound sensitivity data sets available from the DTP, were used to empirically determine whether gene-compound correlates of a sufficiently high correlation coefficient would have a suitable low false discovery rate to support the use of a correlative approach and these datasets for early discovery approaches for new targeted therapies.
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: Sixty six cell lines were analysed, with no repetitions. Twelve cell lines were pooled for a common reference.

first: Brian

middle: Z

last: Ring

first: Doug

middle: T

first: Stella

last: Chang


title: IKKa regulated gene expression

status: Public on Feb 06 2008

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary:
Gene expressions of wild-type, IKKa-/- and IKKa+/+ reconstituted MEFs were compared
Keywords: Gene Knockout and reconstituted

overall_design: Illumina arrays, one array per sample

first: Youn-Tae

last: Kwak

first: Liang-Hao

first: Rui

last: Li

first: Chandrani

last: Mukhopadhyay

first: Michael

middle: D

last: Story

first: Udit

last: Verma


title: LongSAGE analysis of wild-type mouse brain regions

status: Public on Feb 05 2008

city: 91191 Gif/ Yvette Cedex

first: Jean-Marc

last: Elalouf

department: IBITEC-S

institute: CEA Saclay

summary:
LongSAGE libraries generated from various brain regions of 8- to 12-week-old male C57BL/6 mice.
Keywords: Micro-dissection, Brain regions, SAGE

overall_design:
Sau3A I was used as the anchoring enzyme and Mme I as the tagging enzyme.
Data are provided after linker removal.

first: Damien

last: Bessiere

first: Camille

last: Brochier

first: Nicolas

last: Caudy

first: Michel

last: de Chaldee

first: Marie-Claude

last: Gaillard


title: GATA-1-regulated erythroid microRNAs

city: Chicago

first: Louis

last: Dore

address: 303 E Superior St., Lurie Bldg 5-250D

department: Feinberg School of Medicine

institute: Northwestern University

summary:
We employed a gene complementation strategy combined with microarray screening to identify miRNAs involved in the formation of erythroid (red blood) cells.  To search for GATA-1-regulated erythroid miRNAs, we used the Gata-1– erythroblast line G1E.  These cells proliferate in culture as immature erythroid precursors and undergo terminal maturation when GATA-1 activity is restored.  G1E-ER4 is a sub-line stably expressing an estrogen-activated form of GATA-1 (GATA-1 fused to the ligand binding domain of the estrogen receptor).  Treatment of G1E-ER4 cells with estradiol induces a GATA-1-regulated program of gene expression with concomitant cellular maturation.  We used a microarray to evaluate the expression of 292 different miRNAs in G1E-ER4 cells at 0 versus 24 hours after GATA-1 activation.  Affymetrix gene expression profiling has previously been deposited (GEO accession no. GSE628).
Keywords: microRNA analysis of a cell-line model of erythroid maturation

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Two condition experiment, 3 replicates each (independently grown and harvested) of untreated and estradiol-treated (24hrs) G1E-ER4 cells, which express an estrogen-responsive form of the GATA-1 transcription factor.  Each sample is compared to a common reference sample, comprised of an equal mixture of all 6 experimental samples.

first: Mitchell

middle: J

last: Weiss


title: A linear-mixed model approach to identify expressed single nucleotide polymorphisms using short oligo microarrays

first: Nicholas

last: Hardison

summary:
Background: Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed with Affymetrix porcine microarrays is presented. A linear mixed model analysis was used to identify significant breed-by-probe interactions.   Results:  Gene specific linear mixed models were fit to each of the log2 transformed probe intensities on these arrays, using fixed effects for breed, probe, breed-by-probe interaction, and a random effect for array.  After surveying the day 25 placental transcriptome, 789 probes with a q-value ≤ 0.05 and |fold change| ≥ 2 for the breed-by-probe interaction were identified as candidates containing SFP. To address the quality of the bioinformatics approach, universal pyrosequencing assays were designed from Affymetrix exemplar sequences to independently assess polymorphisms within a subset of probes. Of those probes sampled from high-, medium-, and low-ranking categories, 20 of 27 were confirmed by pyrosequencing to contain SFPs.  In most cases, the 25-mer probe sequence printed on the microarray diverged from Meishan, not occidental crosses. This analysis was used to define a set of highly reliable predicted SFPs according to their probability scores.   Conclusions:  By this method we detected transition and transversion single nucleotide polymorphisms, as well as insertions/deletions.  These results demonstrate that this approach can identify polymorphisms between two breeds and/or lines of any species for which a short oligonucleotide array is available, and can be used to rapidly develop markers for genetic mapping and association analysis in species where high density genotyping platforms are otherwise unavailable.  SNPs and INDELS discovered by this approach have been publicly deposited in NCBI’s SNP repository dbSNP. This method is an attractive bioinformatics tool for uncovering breed-by-probe interactions, for rapidly identifying expressed SNPs, for investigating potential functional correlations between gene expression and breed polymorphisms, and is robust enough to be used on any Affymetrix gene expression platform.
Keywords: Transcriptional profiling of Day 25 porcine placentas

overall_design: 6 samples: Breed (Meishan, Occidental) Placental Tissue, Day 25

first: Steve

last: Bischoff

first: Shengdar

last: Tsai

first: Brad

last: Freking

first: Dan

last: Nonneman

first: Gary

last: Rohrer

first: Jorge

last: Piedrahita


title: SAGE analysis of wild-type mouse brain regions

summary:
SAGE libraries generated from various brain regions of 8- to 12-week-old male C57BL/6 mice.
Keywords: Micro-dissection, Brain regions, SAGE

overall_design: Sau3A I was used as the anchoring enzyme and Bsmf I as the tagging enzyme. Data are provided after linker removal.

last: de Chaldée


title: Lactobacillus reuteri ATCC 55730: Before vs after exposure to 0.5% bile.

city: East Lansing

first: Robert

last: Britton

state: MI

address: 6144 BPS Building  Michigan State University

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary:
Transcriptional profiling of Lactobacillus reuteri ATCC 55730 mid-log cultures before vs after exposure to 0.5% bovine bile (oxgall).
Two sets of array experiments were performed.  One set compared the expression profiles of L. reuteri ATCC 55730 cells before bile exposure vs cells that had been exposed to 0.5% bile for 15 minutes (bile shock).  The other set compared the expression profiles of L. reuteri ATCC 55730 cells before bile exposure vs cells that had begun growing again in the presence of 0.5% bile (bile adaptation).
Keywords: Stress response

overall_design: Two sets of two condition experiments: Set one: before bile treatment and 15 minutes after bile treatment.  Biological replicates: 5 untreated and 5 treated, independently grown and collected.  Two replicates per biological replicate (dye-swap).  Set two: before bile treatment and after the resumption of growth in the presence of bile.  Biological replicates: 5 untreated and 5 treated, independently grown and collected.  Two replicates per biological replicate (dye-swap).

first: Kristi

last: Whitehead

first: James

last: Versalovic

first: Stefan

last: Roos


title: Genetics of internal heat necrosis (IHN) in potato (Solanum tuberosum) via microarray analysis of gene expression

status: Public on Feb 03 2008

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

summary:
Potato plants of the cultivar 'Atlantic', which is IHN-susceptible, were grown in the greenhouse under a 16-hour photoperiod and 22 C day/18 C night temperatures for 46 days, after which they were transferred to growth chambers with a 14-hour photoperiod and normal (20 C day/18 C night) temperatures.               At 71 DAP (days after planting), half of the plants were subjected to high (28 C day/20 C night) temperatures for the remainder of the study.  Tubers from both normal and high temperature regimes were harvested at two-week intervals, beginning at 76 DAP and ending at 118 DAP.  For each RNA sample, equal amounts of peeled tuber tissue (sampled from the center of the tuber using a cork borer) was pooled from three randomly chosen plants.  RNA was extracted using a hot-phenol and high salt (2.4 M) CTAB-based extraction buffer.
Keywords: Loop design

overall_design: 16 hybs total

first: Yencho

last: Craig


title: Genetic Analysis of opaque 2 Modifier Loci in Quality Protein Maize

city: Tucson

first: David

middle: Richard

last: Holding

state: AZ

address: 303 Forbes Building

institute: University of Arizona

summary:
Quality Protein Maize (QPM) was created by selecting for genetic modifiers that convert the starchy endosperm of an opaque2 (o2) mutant to a hard, vitreous phenotype.  Genetic analysis has shown there are multiple, unlinked o2 modifiers (Opm), but their identity and mode of action are unknown.  A microarray hybridization performed with RNA obtained from true breeding o2 progeny with vitreous and opaque kernel phenotypes identified a small group of differentially expressed genes, some of which map at or near the Opm QTLs.
Keywords: Genetic modification

overall_design: Compared 18 days after pollination endosperm transcript profiles in true breeding modified (vitreous; V) and non-modified (opaque; O) opaque 2 kernels. Used four vitreous biological reps (V1-V4) and four opaque biological reps (O1-O4). Each biological rep is a pool of 25 kernels representing 5 kernels form each of 5 uniform phenotype ears (vitreous or opaque). Four arrays used: Array 1= V1 vs O1, Array 2 = V2 vs O2, Array 3 = V3 vs O3, Array 4 = V4 vs O4

first: Brian

last: Larkins


title: Expression profiling of T.rubrum treated with Terbinafine

status: Public on Feb 04 2008

city: Beijing

first: Qi

last: Jin

address: Rongjing East Road 6#

country: China

institute: State Key Lab of Virus Gene Engineering

summary:
One antifungal agent, terbinafine(TRB), has specific activity against dermatophytes.A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and transcriptional profiles of the responses to TRB were determined. Some class-specific and mechanism-independent changes in gene expression were found.
Keywords: original article

overall_design: The expression profiles of Trichophyton rubrum treated with TRB were compared to those of Trichophyton rubrum without drug. Each treatment has three replicates.


title: Transcriptome Profiling of Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola on two different medias

city: Davis

first: Malinee

last: Sriariyanun

address: 451 East Health Sciences Drive

department: Plant Pathology

institute: University of California, Davis

summary:
Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) are important bacterial pathogens of the worldwide staple and grass model, rice. Xoo invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice throughout the world. Xoc colonizes the parenchyma tissue to cause bacterial leaf steak, a disease of emerging importance. We have designed oligonucleotide probes (50-70-mers) represented 2,858 Xoo genes and 1,816 Xoc genes annotated by The Institute for Genomic Research (TIGR). To validate the Xo arrays, self-hybridization samples and tests of the non-specific hybridization using randomly spotted oligonucleotides corresponding to the hygromycin phosphotransferase gene (hph), and blank spot and of the correlation coefficient between biological replicates as well as between duplicate spots revealed that the data generated from our oligo array were highly reliable and consistent. To demonstrate application of Xo array, we performed expression profiling experiments on arrays hybridized with RNA of Xoo and Xoc grown in the two different nutrient-condition media. Several sets of genes involved in bacterial movement, chemotaxis, and hrp genes differentially express in response to different treatment. Due to comprehensive views of microarray study, extended biological events of plant-bacteria interaction was described. This publicly available microarray for Xanthomonas oryzae (Xo) is an enabling resource for a large and international community of scientists to better understand not only Xo biology but also many other Xanthomonas species that cause significant losses on crops.
Keywords: Media condition response

sample_organism: Xanthomonas oryzae pv. oryzae KACC 10331

overall_design: Two different types of medias, PSB and XOM2, are used for culturing both Xoo and Xoc. 3 biological replicates and dye-swap replicates. 6 slides per experiment

first: Young-Su

last: Seo

first: Li

last: Wang

first: Jirapa

last: Phetsom

first: Ki-Hong

last: Jung

first: Michael

last: Shultz

first: H

last: Chou

first: Adam

last: Bogdanove

first: Pamela

last: Ronald


title: BCR/ABL1-Dependent Transcriptional Response Reveals Enrichment for Genes Involved in Negative Feedback Regulation

status: Public on Feb 01 2008

city: Lund

first: Petra

last: Johnels

address: Lund University Hospital

department: Clinical Genetics

country: Sweden

institute: Lund University

summary:
Philadelphia (Ph) chromosome-positive leukemia is characterized by the BCR/ABL1 fusion protein that affects a wide range of signal transduction pathways. The knowledge about its downstream target genes is, however, still quite limited. To identify novel BCR/ABL1-regulated genes we used global gene expression profiling of several Ph-positive and Ph-negative cell lines treated with imatinib. Following imatinib treatment, the Ph-positive cells showed decreased growth, viability, and reduced phosphorylation of BCR/ABL1 and STAT5. In total, 142 genes were identified as being dependent on BCR/ABL1-mediated signaling, mainly including genes involved in signal transduction, e.g. the JAK/STAT, MAPK, TGFB and insulin signaling pathways, and in regulation of metabolism. Interestingly, BCR/ABL1 was found to activate several genes involved in negative feedback regulation (CISH, SOCS2, SOCS3, PIM1, DUSP6, and TNFAIP3), which may act to indirectly suppress the tumor promoting effects exerted by BCR/ABL1. In addition, several genes identified as deregulated upon BCR/ABL1 expression could be assigned to the TGFB and NFkB signaling pathways, as well as to reflect the metabolic adjustments needed for rapidly growing cells. Apart from providing important pathogenetic insights into BCR/ABL1-mediated leukemogenesis, the present study also provides a number of pathways/individual genes that may provide attractive targets for future development of targeted therapies.
Keywords: global gene expression profiling, Ph chromosome, BCR/ABL1, imatinib mesylate

overall_design: Five Philadelphia-positive (Ph+) and five Philadelphia-negative (Ph-) cell lines were cultured in the absence or presence of 1 microM imatinib mesylate for 3 and 12 hours. Total RNA was extracted from untreated and treated cell cultures at both time points, resulting in 4 samples per cell line. RNA extraction, labeling, hybridization, washing, scanning, and feature analysis were performed as described (Håkansson et al., 2008, Genes Chromosomes Cancer). Dye-swap labeling was performed in 32 out of 40 samples. In total, 72 slides were hybridized and scanned. The transcriptional response was studied using the mean value of the 3 and 12 hour microarray measurements.

last: Håkansson

first: Björn

last: Nilsson

first: Anna

last: Andersson

first: Carin

last: Lassen

first: Urban

last: Gullberg

first: Thoas

last: Fioretos


title: Barley low temperature stress

status: Public on Feb 02 2008

city: Riverside

first: Livia

last: Tommasini

address: 2150 Batchelor Hall

department: Botany and Plant Science

institute: University of California, Riverside

summary:
In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Morex to low temperature, including triplicated measurements of cold, freeze/thaw cycles and de-acclimation over 33 days.
Keywords: stress response

overall_design: Plants were grown at 20ºC for seven days and subject to a symmetrical cycle of acclimation, cold, freeze-thaw, and deacclimation. Chilling began by decreasing the temperature overnight from 20ºC to 4ºC at a rate of 1.3ºC•h-1 and maintaining temperatures of 4 ºC in the day and 2ºC at night for 5 days. Freeze-thaw cycling lasted 12 days with day temperatures of 4ºC and night temperatures gradually decreasing from -2ºC the first night to -4ºC for three nights and -10ºC for four nights, then recovering to -4ºC for three nights and -2ºC for one night. This treatment was designed to allow daily freeze-thaw cycling and protein synthesis. Chilling conditions (4ºC day, 2ºC night) were resumed for five days, followed by deacclimation with increasing temperature to 20ºC overnight and maintaining for three days. Sampling was done at four different times, each at the 11th hour of light to avoid circadian effects: 1) before chilling treatment, 2) five days after initiation of chilling treatment, 3) eight days into freeze-thaw treatment and 4) three days into de-acclimation.


title: Post-alcoholism and post-hepatitis C cirrhosis

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

institute: Faculty of Medicine and Pharmacy

summary:
The aim of this study is to compare post-hepatitis C virus (HCV) and post-alcoholism cirrhosis gene expression profiling. By transcriptome analysis with a cDNA array virtually covering every transcript in liver, we compared transcript levels in alcoholic- , HCV-cirrhosis and control liver. A stringent selection identified a list of 70 transcripts which completely separated the 3 groups of patients (7 HCV-cirrhosis, 7 alcoholic cirrhosis and 8 control livers). In contrast, in an hepatocellular carcinoma (HCC) context, comparison of 10 HCV-cirrhosis, 10 alcoholic cirrhosis and the 8 control livers failed to identify such transcripts. We report that dysregulations at the transcriptional level do exist in HCC-free cirrhosis, are transiently observed prior to detectable HCC.
Keywords: etiology-dependent and HCC-dependent analysis

overall_design: Cirrhosis samples were analyzed for 14 patients without hepatocellular carcinoma (alcoholic cirrhosis : A1-A7 and HCV-cirrhosis : V8-V14) and for 20 patients with hepatocellular carcinoma (peritumoral alcoholic cirrhosis : PA1-PA10 and peritumoral HCV cirrhosis : PV11-PV20). Eight control livers (CL1-CL8) have been included. All data in the current study were obtained from 3 separate hybridizations per RNA sample (except for A7 : 2 replicates).

first: F

last: Caillot

first: C

last: Derambure

first: P

last: Bioulac-Sage

first: A

last: François

first: M

last: Scotte

first: O

last: Goria

last: Hiron

last: Daveau

first: J

last: Salier


title: DEPS-1 promotes P granule assembly and RNA interference in C. elegans germ cells

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

summary:
P granules are germ-cell-specific cytoplasmic structures containing RNA and protein and required for proper germ cell development in C. elegans.  A new P-granule-associated protein, DEPS-1, whose loss disrupts P granule structure and function was analysed in this study.  Genome wide analysis of gene expression in deps-1 mutant germ lines identified additional targets of DEPS-1 regulation, many of which are also regulated by the RNAi factor RDE-3.  Our studies suggest that DEPS-1 is a key component of the P granule assembly pathway and that its roles include promoting accumulation of some mRNAs, such as glh-1 and rde-4, and reducing accumulation of other mRNAs, perhaps by collaborating with RDE-3 to generate endogenous short interfering RNAs (endo-siRNAs).
Keywords: Mutant analysis of deps-1 dissected C. elegans gonads

overall_design: We isolated dissected gonads from deps-1 mutant adults and compared each to wild type dissected gonads.  RNA was linearly amplified prior to labeling for all genotypes.  The comparisons were done in quadruplicate on independently grown and isolated animals.

first: Caroline

last: Spike

first: Jason

last: Bader

first: Susan

last: Strome


title: Deinococcus radiodurans R1: wildtype strains vs. oxyR disruption strains

city: Hangzhou

first: Yuejin

last: Hua

state: Zhejiang

address: 268 KaiXuan Road

department: Institute of Nuclear-Agricultural Sciences

institute: Zhejiang University

summary:
In Deinococcus radiodurans, a previously unreported special characteristic of DrOxyR (DR0615) is found with only one conserved cysteine. dr0615 gene mutant is hypersensitive to H2O2, but a little to ionizing radiation. Site-directed mutagenesis and subsequent in vivo functional analyses revealed that the conserved cysteine (C210) is necessary for sensing H2O2, but its mutation did not alter the binding characteristics of OxyR on DNA. Under oxidant stress, DrOxyR is oxidized to sulfenic acid form, which can be reduced by reducing reagents. In addition, quantitative real-time PCR and global transcription profile results showed that OxyR is not only a transcriptional activator (e.g., katE, drb0125), but also a transcriptional repressor (e.g., dps, mntH).
Transcriptional profiling of  comparing wildtype strains with oxyR disruption strains under normal growth conditions.
Keywords: Genetic modification

overall_design:
All genes are identified as described in the published genome sequence (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Deinococcus_radiodurans). PCR primer were designed by PRIMEGENS software and 2996 pairs of gene-specific primers were obtained. The rest specific primers were designed by Primer3 and screened through Blastn. In total, 3096 pairs of primers were synthesized. PCR products were generated and purified, yielding a collection of 3084 distinct open reading frames (single band).
Microarrays were scanned using a GenePix 4000B. GenePix Pro 5.1 was used to quantify hydridization signals. Prior to channel normalization, microarray outputs were filtered to remove spots of poor singal quality by excluding those data points with a mean intensity less than two standard deviations above background in both channels.
Normalization and statistical analysis were carried out in the R computing environment using the linear models for microarray data package (Limma). Within Limma, global LOESS normalization was carried out for each microarray. The 2-replicate spots per gene in each array were used to maximize the robustness of differential expression measurement of each gene via the "lmFit" function within Limma.
One-condition experiment, wildtype strains vs. oxyR disruption strains. Four biological replicates were carried out.

first: Songnian

last: Hu

first: Huan

last: Chen


title: Pathways change in expression during replicative aging in Saccharomyces cerevisiae

city: Claremont

first: Laura

middle: L. Mays

last: Hoopes

address: 175 6th Street

department: Biology

institute: Pomona College

summary:
Yeast replicative aging is a process resembling replicative aging in mammalian cells.  During aging, wild type haploid yeast cells enlarge, become sterile, and undergo nucleolar enlargement and fragmentation; we sought gene expression changes during the time of these phenotypic changes.   Gene expression studied via microarrays and qPCR has shown reproducible, statistically significant changes in mRNA of genes at 12 and 18-20 generations.  Our findings support previously described changes towards aerobic metabolism, decreased ribosome gene expression, and a partial Environmental Stress Response.  Our novel findings include a pseudo-stationary phase, down-regulation of methylation-related metabolism, increased Nucleotide Excision Repair related mRNA, and a strong up-regulation of many of the regulatory subunits of protein phosphatase I (Glc7).  These findings are correlated with aging changes in higher organisms as well as with the known involvement of protein phosphorylation states during yeast aging.  J Gerontol, Jan, 2008, vol 63A, no. 1.
Keywords: aging time course

overall_design: Comparison of gene expression in yeast aging in a mating type W303 wild type using seven microarrays each of 1, 12, and 18-20 generations and six microarrays of 8 generations.  In each case, conditions-matched control young cell samples were used to avoid differential induction of stress response genes.

first: Gloria

last: Yiu

first: Alejandra

last: McCord

first: Alison

last: Wise

first: Rishi

last: Jindal

first: Jennifer

last: Hardee

first: Allen

last: Kuo

first: Michelle

middle: Y

last: Shimogawa

first: Laty

last: Cahoon

last: Wu

first: John

last: Kloke

first: Johanna

last: Hardin


title: Arabidopsis plants exposed to combined heat and drought stress

city: Oak Ridge

first: David

last: Weston

department: Environmental Sciences Division

institute: David Weston

summary:
One of the eminent opportunities afforded by modern genomic technologies is the potential to provide a mechanistic understanding of the processes by which genetic change translates to phenotypic variation and the resultant appearance of distinct physiological traits.  Indeed much progress has been made in this area, particularly in biomedicine where functional genomic information can be used to determine the physiological state (e.g., diagnosis) and predict phenotypic outcome (e.g., patient survival).  Until now, ecology has lacked an analogous approach where genomic information can be used to diagnose the presence of a given physiological state (e.g., stress response) and then predict likely phenotypic outcomes (e.g., stress tolerance, fitness).  We demonstrate that a compendium of genomic signatures can be used to classify the plant abiotic stress phenotype in Arabidopsis according to the architecture of the transcriptome, and then be linked with gene coexpression network analysis to determine the underlying signaling pathways and ultimately the genes governing the phenotypic response. Here, we release microarray data from an expression profiling study where plants were exposed to heat and drought alone, and in combination with each other.
Keywords: Stress response, heat, drought, combined stress

overall_design: A direct loop design with 6 biological replicates for control, heat, drought, and combined heat and drought was performed.  A schematic describing the design is provide as supplementary information.

first: Lee

middle: E

last: Gunter

first: Alistair

last: Rogers

first: Stan

last: Wullschleger


title: Global profiling of developmental gene expression in Myxococcus xanthus

city: Marburg

first: Lotte

last: Sogaard-Andersen

address: Karl-von-Frisch-Str.

department: Ecophysiology

country: Germany

institute: Max Planck Institute for Terrestrial Microbiology

summary:
In response to starvation, Myxococcus xanthus initiates a developmental program that results in the formation of spore-filled multicellular fruiting bodies. Here we have used cDNA microarray analysis to determine changes in the global gene expression at different time points of the developmental process. The expression of nearly 900 genes was found to be altered at least two-fold during development as compared to vegetative cells.  Genes encoding proteins with typical vegetative functions such as protein synthesis and energy metabolism were transcriptionally down-regulated in the early stages of development. Among the 430 genes transcriptionally up-regulated during development genes with regulatory functions were overrepresented; underlining that fruiting body formation relies on a complex signalling network. Notably, almost 40% of all genes with increased expression at different stages of development encoded hypothetical proteins indicating a large unexplored potential of proteins important for fruiting body formation.
Keywords: Time course of development with 9 time points

overall_design: 3 biological replicates each; normalized ratios to vegetative cells of  DK1622 (wt) Cy5

first: Nils

last: Hamann

first: Sigrun

last: Wegener-Feldbrügge

first: Reiner

last: Hedderich


title: Genomic profiles of Macaca fascicularis exposed to Venezuelan equine encephalitis

city: Silver Spring

first: Rasha

last: Hammamieh

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

summary:
Gene expression analysis of PBMC exposed to VEE
Keywords: VEEV challenge in Monkey

overall_design: Six treatments (in vivo) at 3, 4 and 14 days compared with 25 controls


title: Porphyromonas gingivalis: Control (Wild-type W83) vs. its htrA mutant

city: Gainesville

first: Paulo

last: Rodrigues

state: FL

address: 1600 Archer Rd

department: Oral Biology

institute: University of Florida

summary:
Transcriptional profiling of the wild-type and its htrA mutant. Identification of genes that are affected by the htrA mutation in P. gingivalis
Keywords: Genetic modification

overall_design: Two-condition experiment, W83 vs. htrA mutant late-log growth phase. Biological replicates: 4 control, 4 mutant, independently grown. One replicate per array.


title: Gene expression variation in lymphocyte subpopulations in response to low dose of ionizing radiations

city: Fontenay aux Roses Cedex

first: Gaetan

last: GRUEL

address: BP 17

department: Service de RadioBiologie et d'Epidemiologie

institute: Institut de Radioprotection et de Surete Nucleaire

summary:
Lymphocytes are the standard cell of a majority of biodosimetry approaches because of their availability and radiosensitivity. But progresses remain to be performed to bring down the minimum threshold of dose sensitivity. To find a lymphocyte subtype able to respond to low doses of ionizing radiation, we examined gene expression variations in different lymphocyte subpopulations using the microarray technology. Blood samples were independently exposed to 0, 0.05 and 0.5 Gray of ionizing radiations. Three and 24 hours after exposure, CD56+, CD4+ and CD8+ cells were negatively isolated. RNA from each condition was competitively hybridized on oligonucleotide microarrays.
Keywords: Dose response, stress response, cell type comparison

overall_design: We characterized genes whose expression level was affected following exposure to γ rays by carrying out genome-wide expression profiling on each lymphocyte subpopulation. Total blood samples were collected from 5 healthy male donors. Each sample was splitted into three parts which were exposed respectively to 0 Gy (sham-irradiated), 0.05 Gy and 0.5 Gy of ionizing radiations. Lymphocytes subpopulations were sorted 3 and 24 hours after irradiation. RNA was prepared from each cell type and amplified. The amino-allyl amplified RNAs were labeled and independently hybridized to the array. RNA from MNC obtained from 20 independent healthy donors constituted the reference group for competitive oligonucleotide microarray hybridization. According to our criteria of quality, we considered a total of 114 microarrays

first: Pascale

last: VOISIN

first: Xavier

last: GIDROL

first: Laurence

last: ROY


title: 19 K14Cre; p53F/F mouse mammary tumor analysis

city: South San Francisco

first: Christiaan

middle: Nicolaas

last: Klijn

address: 1 DNA Way

department: Bioinformatics and Computational Biology

country: Netherlands

institute: Genentech

type: Genome variation profiling by genome tiling array

summary:
Tumor formation is in part driven by copy number alterations (CNAs), which can be measured using array Comparative Genomic Hybridization (aCGH). Identifying regions of DNA that are gained or lost in a significant fraction of tumor samples can facilitate identification of genes possibly related to the development of cancer. Until now, no method has been described that provides a statistical framework in which these regions can be identified without prior discretization of the aCGH data. Kernel Convolution - a Statistical Method for Aberrant Region deTection (KC-SMART) is a new approach which inputs continuous aCGH data to identify regions that are significantly aberrant across an entire tumor set. KC-SMART uses kernel convolution to generate a Kernel Smoothed Estimate (KSE) of CNAs across the genome, aggregated over all tumors. By varying the width of the kernel function, a scale space is created which enables the detection of aberrations of varying size. In an analysis of 89 human sporadic breast tumors KC-SMART performs better than a previously published method, STAC. Our method not only identified aberrations that are strongly associated with clinical parameters, but also showed stronger enrichment for known cancer genes in the detected regions.  Furthermore, KC-SMART identifies 18 aberrant regions in mammary tumors from p53 conditional knock-out mice. These regions, combined with gene expression micro-array data, point to known cancer genes and novel candidate cancer genes.
Keywords: Comparative Genomic Hybridization, aCGH

overall_design: 19 mouse mammary tumors samples were measured against spleen-derived DNA from the same animal on our in-house aCGH platform. Goal of the study was to assess recurrent genomic aberrations in these tumors. This is a tissue specific knockout of p53. Experiments were perfomed in dye-swap

first: Klijn

last: Christiaan


title: SAGE: gene expression in pigs of two commercial lines at the 3 and  9 months og age

city: trieste

first: simeone

last: dal monego

address: piazzale valmaura 9

department: biology

institute: university of trieste

summary:
Muscle development is associated with a modification of mass, composition and function that in productive animals are considered responsible of meat characteristics. In this study, SAGE was employed to describe gene expression in pigs of two commercial lines at the 3 and  9 months og age. The aim was to obtained a full gene expression profile that would assist in identifying genes differentially expressed in the muscle Longissimum dorsi during normal growth. The pattern of expression between lines and ages will help to elucidate the metabolic pathways modulated by these genes during muscle development.
Keywords: SAGE, muscle, swine, age comparison, swine comparison

overall_design:
Twenty castrate pigs, 10 purebred Large White (LW) and 10 Landrace X Duroc (DU), were reared from 3 to 12 months of age in the same environmental and feeding conditions were used.
At the age of  3 and 9 month of age, Longissimum dorsi biopsy was collected from each animal of the two groups, using a Magnum Biopsy System (Bard, Covington, GA USA).
SAGE libreries were constructed for the biopsies sampled at 3 and 9 from the one Large White  and one LandraceXDuroc pig. Animals were selected on the basis of the live weight and daily gains, to have the most “fat” Large White and “lean” LandraceXDuroc.

first: Alberto

last: Pallavicini

first: Bruno

last: Stefanon

first: Simeone

last: Dal Monego


title: Barley drought stress

first: Livia

last: Tommasini

summary:
In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Morex to drought over 21 days based on five triplicated stress treatments and a wide range of soil water content treatments.
Keywords: repeat sample

overall_design: Three control were collected at 91% SWC. Five soil water content conditions (SWC) were examined (approximately 68% SWC, 38% SWC,  20% SWC, 11% SWC and 9% SWC) and three samples were analysed for each of these.


title: Effect of AdpA deficient

city: Bunkyo-ku

first: Yasuo

last: Ohnishi

state: Tokyo

address: 1-1-1 Yayoi

department: Biotechnology

institute: University of Tokyo

summary:
Comparative hybridization of wild type versus AdpA deficient mutant
Keywords: Cell type comparison

sample_organism: Streptomyces griseus subsp. griseus NBRC 13350

overall_design: 4 x dual channel slides, dye swap

first: Atsushi

last: Yamashita

first: Jun

last: Ishikawa

first: Hirofumi

last: Hara

first: Hirokazu

last: Suzuki

first: Miwa

last: Ikenoya

first: Haruo

last: Ikeda

first: Hasahira

last: Hattori

first: Sueharu

last: Horinouchi


title: Temporal microarray analysis of Dehalococcoides ethenogenes during the transition into the stationary phase

city: Dübendorf

first: David

middle: R

last: Johnson

address: Uberlandstrasse 133

department: Environmental Microbiology

country: Switzerland

institute: Eawag

summary:
Dehalococcoides bacteria can reductively dehalogenate a wide range of halogenated organic pollutants. In this study, DNA microarrays were applied to monitor dynamic changes in the transcriptome as Dehalococcoides ethenogenes strain 195 transitioned from exponential growth into the stationary phase. In total, 415 non-redundant genes were identified as differentially expressed. As expected, genes involved with translation and energy metabolism were down-regulated while genes involved with general stress response, transcription, and signal transduction were up-regulated. Unexpected, however, was the 8- to 10-fold up-regulation of four putative reductive dehalogenases (RDases) (DET0173, DET0180, DET1535, and DET1545). Another unexpected finding was the up-regulation of a large number of genes located within integrated elements, including a putative prophage and a muti-copy transposon. Finally, genes encoding the dominant hydrogenase-RDase respiratory chain of this strain (Hup and TceA) were expressed at stable levels throughout the experiment, providing molecular evidence that strain 195 can uncouple dechlorination from net growth.
Keywords: time course, stationary phase

overall_design: Dehalococcoides ethenogens strain 195 was grown in batch-pure cultures with TCE as the electron acceptor, hydrogen as the electron donor, and acetate as the carbon source. Parallel biological cultures were sacrificed and RNA was extracted at different times after inoculation. These times corresponded to the early exponential, late exponential, transition, early stationary, and late stationary growth phases. Microarrays were then used to compare the transcriptome during these different growth phases. Genes were identified as differentially expressed if they were more than 2-fold up-regulated or down-regulated between any two time-points during the experiment. In addition, differentially expressed genes had to have a false discovery rate less than 1% and an absolute hybridization signal intensity greater than 300 during at least one time point. Genes that met these conditions were further characterized with hierarchical clustering and COG analysis.

first: Eoin

last: Brodie

first: Alan

last: Hubbard

first: Gary

last: Andersen

first: Stephen

last: Zinder

first: Lisa

last: Alvarez-Cohen


title: Clostridium difficile strain 630 against various strains from different hosts

city: Ithaca

first: Tavan

last: Janvilisri

state: NY

address: Veterinary Research Tower, College of Veterinary Medicine, Cornell University

institute: Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University

summary: Clostridium difficile is a gram-positive, spore-forming enteric anaerobe which can infect humans and a wide variety of animal species. Recently, the incidence and severity of human C. difficile infection has markedly increased. In this study, we evaluated the genomic content of 73 C. difficile strains isolated from humans, horses, cattle, and pigs by comparative genomic hybridization with microarrays containing coding sequences from C. difficile strains 630 and QCD-32g58. The sequenced genome of C. difficile strain 630 was used as a reference to define a candidate core genome of C. difficile and to explore correlations between host origins and genetic diversity. Approximately 16% of the genes in strain 630 were highly conserved among all strains, representing the core complement of functional genes defining C. difficile. Absent or divergent genes in the tested strains were distributed across the entire C. difficile 630 genome and across all the predicted functional categories. Interestingly, certain genes were conserved among strains from a specific host species, but divergent in isolates with other host origins. This information provides insight into the genomic changes which might contribute to host adaptation. Due to a high degree of divergence among C. difficile strains, a core gene list from this study offers the first step toward the construction of diagnostic arrays for C. difficile.

overall_design: Dye-swap experiments with genomic DNA of tested and reference strains

first: Joy

last: Scaria

first: Yung-Fu

last: Chang


city: Kansas City

first: Alexander

middle: V

last: Dmitriev

state: KS

address: 3901 Rainbow Boulevard

institute: Kansas University Medical Center

summary:
Rgg-dependent transcriptional regulation in Streptococcus pyogenes strains MGAS5005 and CS101 was analyzed during post-exponential phase of growth
Keywords: strain comparion, post-exponential growth, rgg mutant

overall_design: Microarray analysis was performed using RNA samples isolated from wild-type MGAS5005 and CS101 strains as well as their rgg mutant strains during post-exponential phase of growth

first: Emily

last: McDowell

first: Brienne

last: Lineweber

first: Kyle

last: Kappeler

first: Michael

middle: S

last: Chaussee


title: Transcription profiling of soybean nodulation by Bradyrhizobium japonicum

city: Urbana

first: min

last: li

address: Rm230 1101 W peabody Dr

institute: University of Illinois at Urbana-Champaign

summary:
Legumes interact with nodulating bacteria that convert atmospheric nitrogen into ammonia for plant use. This nitrogen fixation takes place within root nodules that form after infection of root hairs by compatible rhizobia. Using cDNA microarrays, we monitored gene expression in soybean (Glycine max) inoculated with the nodulating bacterium Bradyrhizobium japonicum 4, 8, and 16 days after inoculation (dai), time points that coincided with nodule development and the onset of nitrogen fixation. This experiment identified several thousand genes that were differentially expressed in response to B. japonicum inoculation. Expression of 27 genes was analyzed by qRT-PCR and their expression patterns mimicked the microarray results confirming integrity of analyses. The microarray results suggest that B. japonicum reduces plant defense responses during nodule development. In addition, the data revealed a high level of regulatory complexity (transcriptional, post-transcriptional, translational, post-translational) that is likely essential for development of the symbiosis and adjustment to an altered nutritional status.
Keywords = symbiosis
Keywords = nodulation
Keywords = rhizobium
Keywords = defense
Keywords = ANOVA
Keywords = plant
Keywords: nodulating vs not nodulating

overall_design: loop design, 7 samples, 7 comparison, 2 technical repeats including dye swaps, 4 biological repeats

first: Laurent

last: Brechenmacher

first: Moon-Young

last: Kim

first: Marisol

last: Benitez

first: Min

last: Li

first: Trupti

last: Joshi

first: Bernarda

last: Calla

first: Mei

last: Lee

first: Marc

last: Libault

first: Lila

middle: O

last: Vodkin

first: Dong

last: Xu

first: Suk-Ha

first: Steven

last: Clough

last: Stacey


title: Transcriptomic analysis for Pch/ Ler regulon in enterohaemorrhagic Escherichia coli O157:H7

city: Suita

first: Toru

last: Tobe

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

institute: Osaka University

summary:
Enterohaemorrhagic Escherichia coli (EHEC) is an emerging pathogen that causes diarrhea and heamolytic uremic syndrome. Much of the genomic information that affects virulence is acquired via horizontal transfer. Genes necessary for attaching and effacing lesions are located in the LEE pathogenicity island. LEE gene transcription is positively regulated by Ler, which is also encoded by the LEE, and by Pch regulators, which are encoded at other loci. We identified genes whose transcription profiles were similar to those of the LEE genes, by comparing the effects of altering ler and pch transcript levels. We assigned these genes into two classes, according to their transcription profiles.
Keywords: Genetic modification

overall_design: 13 sets of comparison between transcription profiles in strains with different pch or ler genotypes. Labelling of cDNA and hybridization were performed twice with independently prepared RNAs.

first: Hiroyuki

last: Abe


title: Effect of in ovo feeding on late-term turkey embryo ileum gene expression profiling

status: Public on Jan 31 2008

city: Raleigh

first: Jean

middle: Eduardo

last: de Oliveira

address: 2711 Founders Dr

department: Poultry Science

institute: North Carolina State University

summary:
Turkey embryos are very sensitive to perturbations in energy metabolism because they have a wider hatching window than chicken embryos. Mortality of turkey embryos during late-term incubation is high relative to chickens, and many surviving hatchlings have compromised vitality. Intestinal maturation at hatch is also crucial to survival and post-hatch performance. The study of poultry embryo metabolism during the last stages of incubation is difficult due to many shifts and changes that occur in preparation for hatching. Microarray technology is suitable to study complex biological systems like avian late-term embryonic development. Therefore, the objectives of this study were to create a customized focused oligonucleotide microarray based on chicken genome sequences that could be used to study late-term avian metabolism and intestinal maturation, and use this array to survey turkey embryos gene expression from 20 days of incubation until hatch. The key features of this microarray are that all genes present have been annotated and gene spot replication (4) within each array chip. Microarray analysis was performed on liver, pectoral muscle, hatching muscle, and duodenum
Keywords: time course, embryo development, fed versus non-fed

overall_design: Pooled samples from 4 embryos were arraged on a complete interwoven loop design where each treatment (embryonic ages 22, 24, 25, 26 and 28) was replicated 4 times (2 dye-swaps).

first: Chistopher

middle: M

last: Ashwell

first: Peter

last: Ferket

first: Zehava

last: Uni

first: Shelly

last: Druyan


title: Effect of in ovo feeding on late-term turkey embryo hatching muscle (musculus complexus) gene expression profiling


title: ArcA deletion mutant/MR-1

first: haichun

last: gao

address: 388 Yuhangtang Rd.

summary:
Transcriptional differences between arcA deletion mutant and wild type under aerobic or anaerobic conditions
Keywords: RNA/RNA

overall_design: Cells grown to mid-log phase under aerobic or anaerobic conditions.

first: Haichun

last: Gao


title: Effect of in ovo feeding on late-term turkey embryo duodenum gene expression profiling


title: Acute Lung Injury In Experimental Malaria

city: Toronto

first: Fiona

last: Lovegrove

state: ON

address: 1 King's College Circle, MSB Rm 7318

department: Institute of Medical Science

institute: University of Toronto

summary:
Although respiratory distress is a common complication of severe malaria, little is known about the underlying molecular basis of lung dysfunction. Animal models have provided powerful insights into the pathogenesis of severe malaria syndromes such as cerebral malaria; however, no model of malaria-induced lung injury has been definitively established. This work used bronchoalveolar lavage (BAL), histopathology and gene expression analysis to examine the development of acute lung injury (ALI) in mice infected with Plasmodium berghei ANKA (PbA). BAL fluid of PbA-infected C57BL/6 mice revealed a significant increase in IgM and total protein prior to the development of cerebral malaria (CM), indicating disruption of the alveolar-capillary membrane barrier – the physiological hallmark of acute lung injury (ALI). In contrast to sepsis-induced ALI, BAL fluid cell counts remained constant with no infiltration of neutrophils. Histopathology showed septal inflammation without cellular transmigration into the alveolar spaces. Microarray analysis comparing malaria-induced ALI with sepsis-induced ALI identified several common gene ontology groups characterizing ALI in these models, including defense and immune response. Severity of malaria-induced ALI varied in a panel of inbred mouse strains, and development of ALI correlated with peripheral parasite burden but not CM susceptibility. CD36-/- mice, which have decreased parasite lung sequestration, were relatively protected from ALI. In summary, parasite burden and CD36-mediated sequestration in the lung are primary determinants of ALI in experimental murine malaria. Furthermore, differential susceptibility of mouse strains to malaria-induced ALI and CM indicate that distinct genetic determinants likely regulate susceptibility to these two important causes of malaria-associated morbidity and mortality.
Keywords: Time course

platform_organism:
Plasmodium berghei
Mus musculus

overall_design:
Lungs were excised immediately following euthanasia, snap-frozen in liquid nitrogen and stored at –80°C until use. Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions, and mRNA was purified using an Oligo-dT cellulose column (NEB, Mississauga, ON) as described previously [54]. cDNA with incorporated 5-(3-aminoallyl)-2’deoxyuridine-5’-triphosphate (AAdUTP; Sigma, Oakville ON) was reverse-transcribed from 1-2 µg mRNA. Purified cDNA was coupled with N-hydroxysuccinimide esters of Cy3 or Cy5 (GE Lifesciences, Baie d'Urfe QC). Cy3 and Cy5-labeled cDNA pairs and Agilent control spots were added to a final volume of 0.5ml hybridization buffer (1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate (MES), pH 6.5, 33% formamide and 40µg salmon sperm DNA (Invitrogen)). Hybridizations were performed in Agilent hybridization (Agilent, Palo Alto CA) chambers at 42°C with rotation for 18-24 hours. Slides were washed in 6X SSPE, 0.005% sarcosine, followed by 0.06X SSPE, allowed to dry and scanned with a 4000A microarray scanner (Axon Instruments, Union City CA). TIFF images were quantified with GenePix (Axon Instruments). Variance stabilizing normalization [55] and loess smoothing were applied in Bioconductor [56] and the data were transformed to log2 scale.

Each array was hybridized with cDNA transcribed from an RNA pool of 5 C57BL/6 mice per timepoint (Day 0 and 6) and technical replicates (dye-swap) experiments were performed for both time points.

first: Sina

middle: A

last: Gharib

first: Lourdes

last: Pena-Castillo

first: Timothy

last: Hughes

first: W

middle: C

last: Liles

first: Kevin

last: Kain


title: Effect of in ovo feeding on late-term turkey embryo liver gene expression profiling


title: Revealing Targeted Therapy for Human Cancer by Gene Module Maps

status: Public on Jan 28 2008

city: Stanford

first: David

last: Wong

address: 269 Campus Drive

institute: Stanford University

summary:
A major goal of cancer research is to match specific therapies to molecular targets in cancer. Genome-scale expression profiling has identified new subtypes of cancer based on consistent patterns of variation in gene expression, leading to improved prognostic predictions. However, how these new genetic subtypes of cancers should be treated is unknown. Here we show that a gene module map can guide the prospective identification of targeted therapies for genetic subtypes of cancer. By visualizing genome-scale gene expression in cancer as combinations of activated and deactivated functional modules, gene module maps can reveal specific functional pathways associated with each subtype that might be susceptible to targeted therapies. We show that in human breast cancers, activation of a poor-prognosis wound signature is strongly associated with induction of both a mitochondria gene module and a proteasome gene module. We found that 3-bromopyruvic acid, which inhibits glycolysis, selectively killed breast cells expressing the mitochondria and wound signatures. In addition, inhibition of proteasome activity by bortezomib, a drug approved for human use in multiple myeloma, abrogated wound signature expression and selectively killed breast cells expressing the wound signature. Thus, gene module maps may enable rapid translation of complex genomic signatures in human disease to targeted therapeutic strategies.

Cell Line: Transduced construct
Keywords: cell_type_comparison_design

overall_design: Computed


first: Alexander

last: Dmitriev

summary:
Rgg-dependent transcriptional regulation in SF370 Streptococcus pyogenes strain was analyzed during post-exponential phase of growth
Keywords: rgg mutant

overall_design: Microarray analysis was performed using RNA samples isolated from both wild-type SF370 and SF370 rgg mutant strains during post-exponential phase of growth

first: Emily

last: McDowell

first: Brienne

middle: N

last: Lineweber

first: Kyle

last: Kappeler

first: Michael

last: Chaussee


title: Whole-genome transcriptional profiles of SGIV both in vitro and in vivo

city: Guangzhou

first: yong

last: teng

address: 135 West Xingang Road

institute: Sun yet-san university

summary:
Singapore grouper iridovirus (SGIV) is the major agent that causes severe iridovirus diseases in grouper maricluture. Based on the genomic information, a DNA microarray, containing probes corresponding to 162 putative SGIV open reading frames (ORFs), was constructed to map the viral gene transcriptional profiles over the time course by establishing the models of SGIV-infected GS cells and SGIV-infected grouper. All the data from real-time RT-PCR, RT-PCR and dilution RT-PCR assays were confirmed with the findings of microarrays, which were clustered into groups with the similarity expression profiles by the Self-Organizing Maps (SOMs) approach. The microarray analysis showed that SGIV had big differential expression profiles in the special infected cells and organ and the viral DNA replication mechanisms were firstly prevented as an important strategy of the host defense during the natural course infection.Our studies firstly uncover the relative of a marine viral gene expression patterns between in vitro and in vivo infection, which provides a better understanding of SGIV transcription regulation and a greater degree shared with other iridoviruses on their repliaction and pathogenesis.
Keywords: time course

sample_organism:
Iridovirus
Epinephelus coioides
Epinephelus tauvina

overall_design: To further characterize SGIV gene expression patterns and to monitor the gene temporal kinetic transcription program on a genome-wide scale, we monitored viral gene expression profiles in vitro and in vivo infection.For the experiment of infection in vitro, GS cell monolayers cultured in 75cm2 flask were inoculated with 1ml of SGIV (5.0 ×105.5 TCID50/ml) at 25oC. The mock-infected cells (as reference samples) were treated in the same manner as SGIV-infected cells but with fresh culture medium. Total RNA was isolated from the cells at 1, 2, 4, 6, 8, 10, 12, 16, 24, 36, 48, 72, and 96 hours post-infection (h p.i.), respectively. For the experiment of infection in vivo, Grouper Epinephelus tauvina juveniles with approximately 40-50 g were experimentally infected with 150 µl of the SGIV inoculum (5.0×105.5 TCID50/ml) and held in tanks supplied with running seawater at 25oC. Control fishes were injected with the same volume of EMEM. Total RNA was harvested from the spleens of 5 fishes randomly selected from the experimental population at 1, 2, 3, 4, 5, 7, 9, 11, and 15 days post-infection (d p.i.). Total RNA from the spleens of 35 mock-infected fishes was used as reference samples. After visual inspection for the presence of image artifacts, such as scratches, dirt, contamination, high region, or overall background on the array, the scanned images were saved as TIF files and further analyzed to generate raw data using SpotDataTM software (CapitalBio). After filtering the low-intensity spots and background-noise value, a global scaling procedure was performed to normalize among the different arrays and the different channels of same arrays using housekeeping gene of piscine 18S RNA which was also spotted in triplicate. To estimate the variance result from dye-bias, a swap-dye strategy was used for the virus-infected and mock-infected samples at 48 h p.i.

first: Yong

last: Teng

first: Qiwei

last: Qin


title: profiling of an organ-specific sunflower transcriptoma under abiotic stress (salinity and cold conditions)

status: Public on Jan 29 2008

city: Castelar

first: Paula

last: Fernandez

state: Buenos Aires

address: N. Repetto y Los Reseros S/N

country: Argentina

institute: INTA Castelar

summary:
Sunflower is an important source of vegetable oil worlwide. A differential organ-specific sunflower ESTs was previously generated by a subtractive hybridization method, including a considerable number of abiotic stress associated sequences. The objective of this work is to analyze the sunflower gene expression of previously identified candidate genes under a comprehensive microarray analysis of the leaf transcriptoma under cold and salinity stresses, considering the impacts of these abiotic stresses on sunflower yield in many productive areas.
The aimed of this work is to perform genome analysis of sunflower based on its functional regions and the characterization of the sunflower transcriptoma profiles for different organ-specific genes.  Abiotic-related expressed genes were the target of this characterization through a gene expression analysis of the local EST bank (annotated according to Gene Ontology Annotation) using a cDNA organ-specific microarray chip approach.  We analyzed 287 differentially expressed genes derived from leaf, stem, R1 and R4 flower developmental stages.  Transcriptional analysis allowed the detection of three different groups of genes according to their expression patterns.  Group 1 contained 112 up-regulated genes under abiotic stress conditions (cold or salinity), whereas Group 2 (126 genes) did not show changes in their expression levels. On the other hand, 49 genes were classified as Group 3 included were down-regulated genes under both stresses.
Eighty genes exhibited a significative fold change under abiotic stress conditions, being six of them validated by qRT-PCR.  Microrarray profiling of cold and NaCl-treated sunflower leaves revealed dynamic changes in transcript abundance, including transcription factors, defense/stress related proteins, and effectors of homeostasis, all of which highlight the complexity of both stress responses.  This finding provides identification of many transcriptional processes occurring under abiotic stress in sunflower for genes isolated from organ-specific cDNA libraries
Keywords: gene expression profile of organ-specific sunflower transcriptoma in response to NaCl and cold

overall_design: To control biological variation between individuals, three biological samples from the same tissue were pooled on one sample prior to probe preparation. The reference (control) sample consisted of pooled RNA extracted from sunflower seedlings growing under unaltered environmental greenhouse conditions, whereas chilling and salinity samples were RNA extracted from sunflower seedlings growing in greenhouse under those stressed conditions.  The RNA (800ng) samples were labeled by using SuperScript Indirect RNA Amplification System Kit (Invitrogen, cat# L1016-02) based on the method designed by Eberwine y col. 1992. Following RNA amplification (with the incorporation of UTP aminoallil), labeled product was achieved by incubating with Cy3 or Cy5 esters in alkaline media.  Slides were used in order to quantify the relative expression of ESTs in control and treated leaves by Cy3 and Cy5 hybridization technique Dye-swaps were used to correct for differences in incorporation and fluorescent properties of both dyes, generating a number of 9 slides per experiment (three slides for control and three slides for each treatment) with a total number of 18 slides considering technical replicates.

first: Julio

last: Di Rienzo

first: Horacio

last: Hopp

first: Norma

last: Paniego

first: Ruth

last: Heinz


title: Gene expression variation among eight maize inbreds

status: Public on Jan 26 2008

city: Saint Paul

first: Robert

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

summary:
Expression profiling analyses for eight maize inbreds reveals extensive transcriptional variation.  Many genes exhibit presence-absence variation among the inbred lines.
Keywords: Genotype comparison series

overall_design: Affymetrix expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for eight different inbred lines; B37, B73, B84, Mo17, Oh43, B14a, Wf9 and W22.

first: Nathan

last: Springer


title: Molecular landscape of modified histones in Drosophila heterochromatin

city: Seattle

first: Barbara

last: Wakimoto

state: WA

address: University of Washington, Box 351800

institute: University of Washington

summary:
The aim of this study is to analyze the distribution of the modified histones in and around peri-centromeric heterochromatin at high resolutions for understanding the molecular nature of the heterochromatic genes and euchromatin-heterochromatin transition.
Keywords: ChIP-chip

overall_design: Since heterochromatin is repeat-rich, stringent repeat-filtering was applied in the genome-tiling array design. When possible, parallel analyses were performed with two different types of reference controls, namely total genomic DNA and histone H3 C-terminus ChIP.

first: Jiro

last: Yasuhara

middle: T


title: Classification of three temporal kinetic transcripts of SGIV

summary:
Singapore grouper iridovirus (SGIV) is the major agent that causes severe iridovirus diseases in grouper maricluture. Based on the genomic information, a DNA microarray, containing probes corresponding to 162 putative SGIV open reading frames (ORFs) was constucted. The viral microarrays wereused to classify the majority of SGIV transcripts into three temporal kinetic classes (immediate-early, IE; early, E; late, L) during an in vitro infection by their dependence on de novo protein synthesis inhibitor and viral DNA replication.
Keywords: drug response

sample_organism:
Iridovirus
Epinephelus coioides

overall_design:
To map the SGIV transcripts into temporal kinetic classes during the infection in vitro, GS cells were treated with drug inhibitors as previously described with some slight modifications. Briefly, GS monolayers were treated for 1 h prior to, during and throughout the viral infection with either CHX or PAA, which inhibited de novo protein synthesis and viral DNA replication mechanisms, respectively. To distinguish between viral IE transcripts and other transcripts, cells infected with SGIV (MOI of 5) or mock infected were treated with CHX (100 µg/ml), and then harvested at 8 h p.i. Whereas, viral E and L transcripts were categorized when cells infected with SGIV (MOI of 5) in the presence and absence of PAA (200 µg/ml), respectively. Until at 36 h p.i., cells were
collected for RNA extraction. In a comparison analysis, we used Significance Analysis of Microarrays (SAM) software
to identify the groups of different expression genes between the drug-treated samples and
untreated samples. SAM identifies genes with statistically significant changes in expression by assimilating a set of gene-specific
t tests. Significance is based on an estimated of FDR≤5% and a 2 fold-change cutoff. Only the genes that met the following three criteria could be categorized into various temporal kinetic classes: (i) a viral gene was considered to be a IE transcript if its expression level increased or weakly affected under CHX treatment, (ii) a viral gene was
considered to be a L transcript if its median intensity ratio in the PAA-treated samples was at least two-fold lower than that in the untreated samples and (iii) a viral gene was considered to be a E transcript if it expressed higher or remained within the two-
fold range after PAA treatment but was inhibited distinctly by CHX treatment. To identify the significant differences in gene
expression, a criterion with at least two-fold change combined with student’s one sample t-test p value <0.05 was adopted.


title: Analysis of the group A Streptococcus CcpA Transcriptome

status: Public on Jan 30 2008

city: Houston

first: Samuel

last: Shelburne

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

summary:
This study evaluate how catabolite control protein A (CcpA) inactivation affected gene transcript levels in the group A Streptococcus serotype M1 strain MGAS5005 during growth in standard laboratory medium.
Keywords: transcriptome analysis

overall_design: 4 replicates of strain MGAS5005 and delta_cppA were grown in THY to early and late logarithmic growth phases.  The transcriptomes of each samples were then analyzed.


title: Differential expression of inflammatory and immune response genes in sheep infected with Anaplasma phagocytophilum.

city: Stillwater

first: Patricia

middle: J

last: Ayoubi

state: OK

address: 246 NRC

department: Biochemistry and Molecular Biology

institute: Oklahoma State University

summary:
Anaplasma phagocytophilum is the causative agent of tick-borne fever (TBF) in ruminants and human, equine and canine granulocytic anaplasmosis. A. phagocytophilum modifies host gene expression and immune response. The objective of this work was to analyze differential gene expression in A. phagocytophilum-infected sheep using microarray hybridization and real-time RT-PCR in experimentally and naturally infected animals.
Keywords: disease state analysis

platform_organism:
Sus scrofa
Bos taurus
Ovis aries

overall_design: one-month old lambs from an experimental flock without a known history of contact with ticks and tick-borne pathogens were weaned and left uninfected to serve as controls or infected with a pool of blood samples obtained from commercial flocks with a previous history of TBF, located in the Basque Country, Northern Spain.

first: Ayoubi

last: Patricia


title: Chordoma_32k_1Mb

status: Public on Jan 25 2008

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

institute: Lund University

summary:
Frequent deletion of the CDKN2A locus in chordoma: analysis of chromosomal imbalances using array comparative genomic hybridization

DNA copy number analysis of 21 fresh frozen chordoma biopsies, and the respective relapse in four of them, using 32k and 1Mb array CGH. All cases showed copy number alterations and primarily deletions of chromosomal regions were found. Particularly, the CDKN2A and CDKN2B loci in 9p21 were homo- or heterozygously lost in 70% of the tumors.
Keywords: chordoma, array comparative genomic hybridization

overall_design: Cases 1-11 were analyzed using 32k array CGH and male genomic DNA (Promega) was used as reference. Cases 17-26, and the respective relapse in four of these tumors, were analyzed with 1 Mb array CGH, using sex matched controls.

first: K

last: Hallor

first: J

last: Staaf

first: G

last: Jönsson

first: M

last: Heidenblad

first: F

last: Vult von Steyern

first: H

last: Bauer

last: Ijszenga

first: P

last: Hogendoorn

first: N

last: Mandahl

last: Szuhai

last: Mertens


title: Effect of in ovo feeding on late-term turkey embryo breast muscle (pectoralis major) gene expression profiling

first: Jean

last: de Oliveira

state: NC

first: Chistopher

last: Ashwell

first: Peter

last: Ferket

first: Zehava

last: Uni

first: Shelly

last: Druyan


title: Profiling expression changes caused by a segmental aneuploid in maize

status: Public on Jan 24 2008

first: Nathan

last: Springer

address: 1445 Gortner Ave

department: Plant Biology

summary:
ABSTRACT: BACKGROUND: While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated. RESULTS: We employed a segmental aneuploid condition in maize to study phenotypic and gene expression changes associated with aneuploidy. Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves. The knotted-like homeobox gene knox10, which is located on the short arm of chromosome 5, was shown to be ectopically expressed in developing leaves of the aneuploid plants. Expression profiling revealed that ~40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage. CONCLUSIONS: We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes. A small number of genes exhibit higher levels of expression change not predicted by the dosage, or display altered expression even though they are not located in the aneuploid regions.
Keywords: Genotype comparison of wild-type and segmental aneuploid

overall_design: There are four biological replicates of pooled wild-type siblings and four biological replicates of pooled DpDf plants.  The DpDf plants are segmental aneuploids that contain three copies of the short arm of chromosome 5.  These plants are all in the B73 inbred genetic background.

first: Irina

last: Makarevitch

first: Ronald

middle: L

last: Phillips


title: Genetic homogeneity among strains of Clostridium botulinum type A1 with a unique toxin gene cluster organization

city: Atlanta

first: Brian

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

summary:
Comparative genomic hybridizations were performed to compare bont/A1 strains with an A2-like toxin gene cluster organization to the genome sequenced strain, C. botulinum ATCC 3502.
Keywords: comparative genomic hybridization

overall_design: For each hybridization, the reference strain (C. botulinum ATCC 3502) was labeled with Cy5 and each test strain was labeled with Cy3.

first: Carolina

last: Luquez

first: Loretta

last: McCroskey

first: Lavin

last: Joseph

first: Mark

last: Jacobson

first: Eric

last: Johnson

first: Susan

last: Maslanka

first: Joanne

middle: D

last: Andreadis


title: Copy Number Analysis of Renal Epithelial Neoplasms

first: Federico

last: Monzon

state: TX

address: 6565 Fannin St., MS205

department: Pathology

institute: The Methodist Hospital Research Institute

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
Renal tumors with complex morphology require extensive workup for accurate classification.  Chromosomal aberrations that define subtypes of renal epithelial neoplasms have been reported. We explored if whole-genome chromosome copy number and loss-of-heterozygosity analysis with single nucleotide polymorphism (SNP) arrays can be used to identify these aberrations.
Keywords: Chromosome copy number and LOH analysis with SNP Genotyping Arrays

overall_design: We analyzed 20 paraffin-embedded tissues representing conventional renal cell carcinoma (RCC), papillary RCC, chromophobe RCC, and oncocytoma with Affymetrix GeneChip 10K 2.0 Mapping arrays.

first: Jill

last: Hagenkord

first: Maureen

last: Lyons-Weiler

first: Jyoti

middle: P

last: Balani

first: Anil

last: Parwani

first: Christin

last: Sciulli

first: Jia

last: Li

first: Uma

last: Chandran

first: Sheldon

last: Bastacky

first: Rajiv

last: Dhir