title: Protein phosphatase 2A protects centromeric sister chromatid cohesion during meiosis I

status: Public on May 10 2006

first: Katsuhiko

last: Shirahige

summary:
	Segregation of homologous maternal and paternal centromeres to opposite poles during meiosis I depends on post-replicative crossing over between homologous non-sister chromatids, which creates chiasmata and therefore bivalent chromosomes. Destruction of sister chromatid cohesion along chromosome arms due to proteolytic cleavage of cohesin's Rec8 subunit by separase resolves chiasmata and thereby triggers the first meiotic division. This produces univalent chromosomes, the chromatids of which are held together by centromeric cohesin that has been protected from separase by shugoshin (Sgo1/MEI-S332) proteins. Here we show in both fission and budding yeast that Sgo1 recruits to centromeres a specific form of protein phosphatase 2A (PP2A). Its inactivation causes loss of centromeric cohesin at anaphase I and random segregation of sister centromeres at the second meiotic division. Artificial recruitment of PP2A to chromosome arms prevents Rec8 phosphorylation and hinders resolution of chiasmata. Our data are consistent with the notion that efficient cleavage of Rec8 requires phosphorylation of cohesin and that this is blocked by PP2A at meiosis I centromeres.
Keywords: ChIP-chip, Mitosis, Meiosis, Cell cycle, Saccharomyces cerevisiae, Chromosome VI tiling array, Sgo1, Pp2A, Cse4, Ndc10, Rts1, Rec8

overall_design:
•	Experimental factors
	Distribution of Cse4, Ndc10, Rts1 in mitotic G2 phase and meiosis I (S. cerevisiae). Distribution of Rec8 in meiosis I (S.cerevisiae). All experiments were performed in cells with the same genetic background (Saccharomyces cerevisiae SK1).
•	Experimental design
	ChIP analysis: In all cases, hybridization data for ChIP fraction was compared with SUP (supernatant) fraction. SUP fraction is same as WCE fraction.

•	Quality control steps taken
	Duplication, confirmation using different tags, and different subunits of the same complex. Confirmation of protein distribution using deletion mutant strain. Confirmation of several loci by q-PCR. Checking of the ChIP fraction by Western blotting. Checking of the ChIP fraction by swapping SUP fraction.

Samples used, extract preparation and labelling:
•	The origin of each biological sample
	Saccharomyces cerevisiae (SK1) .

•	Manipulation of biological samples and protocols used
	Chromatin immunoprecipitation (ChIP) and hybridization to Affimetrix high-density oligonucleotide arrays of S. cerevisiae chromosome VI was performed essentially as previously described (Katou et al., 2003, nature) (Lengronne et al., 2004, nature).
•	Technical protocols for preparing the hybridization extract
	The chromatin-immunprecipates were eluted and incubated over night at 65ºC to reverse the cross-link. Immunoprecipitated genomic DNA was incubated with proteinase K, extracted 2 times with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RnaseA. The DNA was then purified using the Qiagen PCR purification kit, and concentrated by ethanol precipitation. The DNA was amplified by PCR after random priming. 10 ug of amplified DNA was digested with Dnase I to a mean size of 100 bp. After Dnase I inactivation at 95ºC. DNA fragments were end-labeled by addition of 25 U of Terminal Transferase and 1 nmol Biotin-N6ddATP (NEN) for 1 hour at 37ºC as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). The entire sample was used for hybridization.
•	Hybridization procedures and parameters:
	Hybridization, blocking and washing were carried out as previously described (http://everythingchromosomevi.gsc.riken.go.jp). Each sample was hybridized to the array in 150 ul containing 6xSSPE; 0.005% TritonX-100; 15 ug fragmented denatured salmon sperm DNA (Gibco-BRL); 1 nmole 3’biotin labelled control oligonucleotide (oligo B2, Affymetrix). Samples were denatured at 100ºC for 10 minutes, and then put on ice before being hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).
•	Measurement data and specifications:

	Arrays were scanned using the Genechip Scanner3000 7G following the library array description. All the raw data files can be downloaded from GEO database. The primary analysis of tiling chip data was performed following exactly the statistical algorithm used for Affymetrix GeneChip Operating Software (GCOS). The detailed information for the algorithm used can be downloaded from the Affymetrix web site at http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf. The analysis is available on request. For the ChrVI array, one unit for analysis (locus) was set to 300bp. Fold change value, change p-value, and detection p-value for each locus were obtained by primary analysis. For the discrimination of positive and negative signals for the binding, we used three criteria as follows. First, the reliability of the signal strength was judged by detection p-value of each locus (p-value≤0.025 for cerevisiae). Secondly, reliability of binding ratio was judged by change p-value (p-value≤0.025 for cerevisiae). Thirdly, clusters consisting of at least 900bp contiguous loci  that satisfied the above two criteria were selected, because it is known that a single site of protein-DNA interaction resulted in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors.

•	Array Design:

		General array design: in situ synthesized arrays by Affymetrix
		Availability of arrays: commercially available from Affymetrix
		Location and ID of each spot on arrays: available from Affymetrix on 			request
		Probe type: oligonucleotide
		The arrays used in this study can be purchased from Affymetrix:
			Chromosome VI S.cerevisiae: rikDACFC6, P/N# 510636

first: Yuki

last: Katou

last: Mori

first: Takehiko

last: Itou

first: Christian

last: Riedel

first: Vittorio

last: Kastis


title: set1, H3K4A, set1htz1, set1htz1sir2 transcription profiles

status: Public on May 17 2006

city: San Francisco

first: Shivkumar

last: Venkatasubrahmanyam

state: CA

department: Biochemistry

country: USA

institute: UCSF

summary:
Relative mRNA abundance of all S. cerevisiae genes was measured in various mutants, compared to wild-type
Keywords: quadruplicate mutant:WT analysis, with dye-swapping

overall_design: mutant and wild-type grown to log phase, YPAD, 30C, purified mRNA, reverse-transcribed to cDNA, labelled with Cy5/Cy3, hybridized to whole genome ORF microarrays

first: Marc

middle: D

last: Meneghini


title: Gene Expression Analysis of Dupuytren's Disease

status: Public on May 19 2006

city: Stanford

first: Andrew

middle: Yuan

last: Zhang

address: 770 Welch Rd, Fourth floor

department: Plastic and Reconstructive Surgery

institute: Stanford Hospital and Clinics

summary:
Dupuytren's disease (DD) is characterized by nodular fibroblastic proliferation of the palmar fascia leading to contracture of the hand. We performed a cDNA microarray analysis of DD palmar  cord tissue.  Normal-appearing palmar fascia adjacent to the diseased cord from the same patient and palmar fascia from patients undergoing carpal tunnel release were used as controls.  A type II microarray experiment was used on amplified sample RNA.  Samples were hybridized to arrays containing 42,000 gene elements. Array data was analyzed with the on-line software from the Stanford Microarray Database.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Type: disease_state_design
Series_overall_design: Computed
Keywords: other

first: Kenton

last: Fong


title: Identification of E47 targets

status: Public on May 09 2006

city: La Jolla

first: Ruth

last: Schwartz

address: Gilman Drive

institute: UCSD

summary:
In maturing T-lineage cells, the helix-loop-helix protein E47 has been shown to enforce a critical proliferation and developmental checkpoint commonly referred to as β selection.  To examine how E47 regulates cellular expansion and developmental progression, we have used an E2A deficient lymphoma cell line and DNA microarray analysis to identify immediate E47 target genes.  Hierarchical cluster analysis of gene expression patterns revealed that E47 coordinately regulates the expression of genes involved in cell survival, cell growth, lipid metabolism, stress response and lymphoid maturation.   These include Cdk6, CD25, Tox, Gadd45a, Gadd45b, Gfi1, Gfi1b, Socs1, Socs3, Id2, Eto2 and Xbp1.  We propose a regulatory network linking JAK/STAT mediated signaling, E47 and SOCS proteins in a common pathway.   Finally, we suggest that the aberrant activation of Cdk6 in E47 deficient T-lineage cells contributes to the development of lymphoid malignancy.
Keywords: gene targets for E47

overall_design: We used the 1F9 cell line, originally isolated from E2A deficient thymomas. To identify E47 target genes, 1F9 cells were transduced with a retrovirus carrying an E47/estrogen receptor (E47ER) hybrid protein.  Control cells were transduced with virus carrying the bHLH region but lacking the N-terminal transactivation domain.  Both retroviral constructs also directed the expression of human CD25 (hCD25) to allow rapid isolation of transduced cells.  One day post-infection, cells were incubated with 4-hydroxytamoxifen (4-OHT) for a period of six hours, to activate the E47ER fusion protein.  hCD25 positive cells were purified using magnetic beads, RNA was isolated and used to generate probes for hybridization to murine oligonucleotide microarrays.

first: Isaac

last: Engel

first: Mohammad

last: Fallahi-Sichani

first: Howard

middle: T

last: Petrie

first: Cornelis

last: Murre


title: EScell data, composed of normalized log ratio of the differentiated compared to the undifferentiated at 5 points

city: Seoul

first: Young Ju

last: Suh

address: Hyochangwon-gil 52, Yongsan-ku

department: Department of Biological Science

country: South Korea

institute: Sookmyung Women's University

summary:
The study of embryonic stem cell mediated neuronal differentiation allows for improved understanding of the mechanisms involved in embryonic neuronal development. We investigated expression profile changes using time course cDNA microarray to identify clues for the signaling network of neuronal differentiation.
Keywords: time course, embryonic stem cell

overall_design: We analyzed the gene expression microarray data, composed of the fluorescent signal intensity ratio, of the differentiated (Cy5 channel; red) compared to the undifferentiated (Cy3 channel; green) at 5 points in time: we started with a treatment with ATRA (Start), 2 days for neuronal induction (2 after), 0 day after the neuronal induction (0 day), 2 days after the neuronal induction (2 days), 7 days after the neuronal induction (7 days).

last: Shim

last: Yang

last: Park


title: Zebrafish promoter microarrays identify actively transcribed embryonic genes

status: Public on May 22 2006

city: Cambridge

first: Elizabeth

last: Herbolsheimer

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

type: Genome binding/occupancy profiling by genome tiling array

summary:
We have designed a zebrafish genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. Using these microarrays, together with chromatin immunoprecipitation with an antibody directed against tri-methylated lysine 4 of Histone H3, we demonstrate the feasibility of this method in zebrafish. This approach will allow investigators to determine the genomic binding locations of DNA interacting proteins during development and expedite the assembly of the genetic networks that regulate embryogenesis.
Keywords: ChIP-chip

overall_design:
Genomic array design
Microarrays were designed as described below and manufactured by Agilent Technologies (www.agilent.com). Further information on design can be found at http://jura.wi.mit.edu/bioc/gbell/zfish_chip/.

Selection of transcription start sites and identification of promoter sequences
We interrogated 5 databases: Ensembl, VEGA, Refseq, ZGC full length clones and a database provided by Dr. Leonard Zon  (Harvard Medical School, Boston, USA) in order to assemble an extensive list of zebrafish transcripts. The Zon lab database is a hand-curated database of zebrafish genes that have homologues in other species. We included all transcripts that appeared in the manually annotated databases (VEGA, Zon) and in the ZGC full length database. We also identified genes present in any 2 of the 5 databases and included those not already selected. The transcripts were mapped to the zebrafish genome (Zv4, June 2004) obtained from UCSC Bioinformatics (http://genome.ucsc.edu) and the transcription start site (TSS) for each transcript was determined. Transcripts with TSSs within 500bp were clustered into a transcriptional unit (TU) and promoter regions were identified relative to the most upstream TSS. This resulted in the identification of 13,413 TUs and corresponding promoter regions.  Each promoter region was extracted and masked for repetitive sequence by RepeatMasker.  If the promoter region contained a gap the upstream sequence was also masked. Information on the transcriptional units that were included in the final design can be found at http://jura.wi.mit.edu/bioc/gbell/zfish_chip/.

Selection of oligonucleotides
60-mer oligonucleotide probes representing the region between 1.5kb upstream and 0.5kb downstream of the annotated TSS of each transcriptional unit were then designed. Although transcription factors and other DNA binding proteins are known to regulate genes from distances of greater than -1.5kb or + 0.5kb, much information can be gained from regions close to the TSS [45],  and the H3K4Me3 mark studied in this paper is found at the most 5’ end of a gene, close to the TSS.

Selection of 60-mers for the microarrays was essentially as described in [14] using the Zv4 build of the zebrafish genome and a locally customized version of ArrayOligoSelector. 60-mers were chosen so that promoter regions contained approximately one probe every 250bp with a maximum distance between probes for each promoter region set at 600bp. In cases where only one probe could be designed for a particular TU these were not included in the final design. This process yielded 80,839 probes for 11,171 promoter regions

We also incorporated several sets of control probes, both positive and negative. On each array there are 1090 probes designed against ‘gene desert’ regions, which are genomic regions that are unlikely to be bound by transcriptional regulators, and 270 probes designed against Arabidopsis thaliana genes, which are not present in the zebrafish genome (by BLAST). In addition, because our main motivation for making these microarrays is to identify mesodermally-regulated genes we included 7 genes expressed in mesoderm during gastrulation as positive controls (wnt11, flh, vent, msgn1, myod, fgf8, pcdh8). Probes designed against these promoters, which flank from 3-4kb around each TSS, are arrayed 2-4 times on each slide. Since these genes are expressed at gastrula stages to varying degrees, they also serve as a positive controls in this study. Finally there are 2256 controls added by Agilent and a variable number of blank spots. These probes were divided between two microarray slides each with 44,290 features.

We refer to these two microarray slides as the ‘proximal promoter set’. A proximal promoter set based on these designs as well as an expanded set of 9 slides which contain regions from –9kb to + 3kb relative to the TSS, are available by contacting Agilent (www.agilent.com) or by downloading the design files from http://jura.wi.mit.edu/bioc/gbell/zfish_chip/ for self-manufacture.

first: Fiona

middle: C

last: Wardle

first: Duncan

last: Odom

first: George

middle: W

last: Bell

first: BingBing

last: Yuan

middle: L

last: Wiellette

first: Timothy

last: Danford

first: Hazel

last: Sive

first: Richard

middle: A

last: Young

first: James

last: Smith


title: Hog1 ChIP Chip

status: Public on May 26 2006

city: Valencia

first: Markus

last: Proft

address: Camino de Vera s/n

department: Inst. Biol. Molecular Celular de Plantas

country: Spain

institute: Universidad Politecnica Valencia

summary:
Yeast Hog1-3HA ChIP-Chip in triplicate
Keywords: ChIP-Chip

overall_design: Yeast Hog1 ChIP-Chip was performed in MAP51 (3HA-Hog1) in triplicate using anti-HA (12CA5 monoclonal antibody)

first: Kevin

last: Struhl


title: Microarray analysis of LRRC3B stable cell derived xenograft tumors

city: Daejeon

first: Mirang

last: Kim

address: 52 Eoeun-dong

department: human genome center

institute: KRIBB

summary:
To understand how LRRC3B exerted tumor supprissive function in tumorigenesis assay, we performed microarray analysis of LRRC3B stable cell derived xenograft tumors.
Keywords: Xenograft tumor

overall_design: LRRC3B stably expressed SNU-601 cells and vector control cells were injected subcutaneously into 3-week-old male nude mice. After 57 days of injection, mice were sacrificed and the tumors were removed. Total RNA was extracted from the xenograft tumors. Twenty µg of xenograft tumor RNA and 20 µg of SNU601 cell line RNA were used as templates for the synthesis of cDNA, labeled with Cy5 or Cy3, using a 3DNA Array 50 kit (Genisphere Inc, Hatfield, PA). 24K cDNA microarray chips containing 23,232 genes and 1,056 controls were hybridized. The hybridized slide was scanned using a GenePix 4000B Scanner (Axon Instruments) and analyzed using the GenePix Pro 4.0 program (Axon Instruments). The raw data were normalized using the print-tip Lowess method available in the marray package of the Bioconductor project (http://www.bioconductor.org)


title: Series1

status: Public on May 01 2006

first: Joe

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary:
This series includes 1 microarray used to detect parainfluenza 4a from an endotracheal aspirate from a patient with acute respiratory failure
Keywords: viral detection

overall_design: The series includes 1 microarray used for viral detection using Viro3 viral detection platform

first: Charles

middle: Y

last: Chiu

first: Silvi

last: Rouskin

first: Anatoly

last: Urisman

first: Jason

last: Merker

first: Bruce

last: Patterson

first: Don

last: Ganem

first: Joseph


title: Methylation profiling of leukemia cell lines

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

type: Methylation profiling by genome tiling array

summary:
Methylation of CpG islands is associated with transcriptional repression and, in cancer, leads to the abnormal silencing of tumor-suppressor genes. We developed a novel and robust technique that allows the unbiased, genome wide detection of CpG-methylation in limited DNA samples, without applying methylation-sensitive restriction endonucleases or bisulfite-treatment. The approach is based on a recombinant, methyl-CpG binding  protein that efficiently binds CpG-methylated DNA depending on its degree of CpG methylation. Its application in methyl-CpG immunoprecipitation (MCIp) facilitates the monitoring of CpG-island methylation on a genome wide level (in combination with CpG-island microarrays). The power of this novel approach was demonstrated by the profiling of three myeloid cell lines leading to the identification of more than a hundred aberrantly methylated CpG islands and many novel, putative tumor-suppressor genes.
Keywords: MCIp on Chip

overall_design: The methylation profiles of the three leukemia cell lines KG-1, U937 and THP-1 were compared to normal human blood monocytes (reference). The set includes three independent hybridizations for each sample.

first: Claudia

last: Gebhard

first: Lucia

last: Schwarzfischer


title: Interference of PrfA with glucose uptake

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

summary:
Listeria monocytogenes (Lm) strains expressing high levels of the virulence regulator PrfA (mutant PrfA* or wild-type PrfA) show strong growth inhibition in minimal media when supplemented with glucose but not when supplemented with glucose-6-phosphate compared to the isogenic strains expressing low levels of PrfA. A significantly reduced rate of glucose uptake is observed in the PrfA* over-expressing strain growing in LB supplemented with glucose. Comparative transcriptome analyses were performed with RNA isolated from a prfA mutant and the isogenic strain carrying multiple prfA or prfA* copies on a plasmid. The analysis reveals in addition to high transcriptional up-regulation of the known PrfA-regulated virulence genes (group I), less pronounced up-regulation in the expression of several phage- and metabolic genes (group II) and strong down-regulation of several genes involved mainly in carbon- and nitrogen- metabolism in the PrfA* over-expressing strain (group III). Among the latter genes are in particular the nrgAB-, gltAB-, glnRA- (involved in nitrogen metabolism), ilvB- operons (involved in biosynthesis of the branched chain amino acids) and genes for some ABC transporters. Most of the down-regulated genes have been shown previously in Bacillus subtilis to belong to a class of genes whose expression is negatively affected by impaired glucose uptake. The results lead to the conclusion that excess PrfA(*) interferes with component(s) essential for PTS-mediated glucose transport.
Keywords: Metabolism and Virulence gene expression

overall_design: Transcriptome analyses were performed using whole genome DNA microarrays that contain synthetic 70mer oligodeoxyribonucleotides covering all ORFs of the Lm genome. Three independent RNA preparations from the conditions to be tested were pooled and 6 equal aliquots (15-20 µg) of total RNA from the strains were used to synthesize cDNA differentially labelled with Cy3-dCTP and Cy5-dCTP (Amersham Pharmacia, Freiburg, Germany) during a first-strand reverse transcription reaction with Superscript II RNase H- RT and 9 µg random primers (Life Technologies, Karlsruhe, Germany). Dye swap was performed as follows: Three cDNA samples from the one strain were generated using Cy3-dCTP and the other three using Cy5-dCTP and similarly for the other strain to be investigated. The two differentially labelled cDNA samples were combined, diluted to 3 × SSC, 0.1% (wt/vol) sodium dodecyl sulfate, hybridized to the microarray slide and incubated at 65°C for 16 hrs. Six such slides were hybridized using the generated probes for each strain combination. In this study there were 3 strain combinations in all.

first: Alexandra

middle: K

last: Marr

first: Biju

last: Joseph

first: Sonja

last: Mertins

first: Regina

last: Ecke

first: Stefanie

last: Müller-Altrock

first: Werner

last: Goebel


title: Gene expression in chicken livers from lean and fat lines

city: Rennes cedex

first: Christian

last: Diot

address: 65, rue de saint-Brieuc, CS 84215

department: Animal Genetics

country: France

institute: INRA

summary:
Fourty RNA samples from the liver of lean and fat line chickens were organized in 10 pools, 4 by 4 and in the order of chicken adiposity. Expression in these pools were compared
Keywords: animals with different genetic background comparison

overall_design: We analyzed 3 arrays for pools 1, 2, 4-7, 9 and 10 and 2 arrays for pools 3 and 8

first: Emmanuelle

last: Bourneuf

first: Frédéric

last: Hérault


title: Danio rerio and Pomacentrus moluccensis: comparative genomic hybridisation and early gene response to heat stress

status: Public on Apr 30 2006

city: Brisbane

first: Karin

middle: Sonja

last: Kassahn

state: QLD

address: Queensland Bioscience Precinct

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

type:
Expression profiling by array
Genome variation profiling by array

summary:
Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we test the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fish species will respond to these increased temperatures and which genes are important for resistance and adaptation to elevated temperatures is not known. Microarray technology may help identify candidate genes for thermal stress resistance in coral reef fishes. Results from a comparative genomic DNA hybridisation experiment and direct sequence comparisons indicate that for most genes there is significant sequence similarity between P. moluccensis and D. rerio, suggesting that the D. rerio array is applicable to P. moluccensis. Heterologous microarray experiments on heat-stressed P. moluccensis identified changes in transcript abundance at 120 gene loci, with many genes involved in protein processing, transcription, and cell growth. Changes in transcript abundance for a selection of candidate genes were confirmed by quantitative real-time PCR. We have demonstrated that heterologous microarrays can be successfully employed to study non-model organisms. Such a strategy thus greatly enhances the applicability of microarray technology to the field of environmental and functional genomics and will be useful for investigating the molecular basis of thermal adaptation in coral reef fishes.
Keywords: stress response, comparative genomic hybridization (CGH)

sample_organism:
Danio rerio
Pomacentrus moluccensis

overall_design:
Common reference design [Stress response_P. moluccensis]: four individual treatment fish (heat-stressed) are contrasted in four microarray hybridisations against a pooled control consisting of four fish kept at ambient temperature. All eight fish employed in this analysis were wild-captured and are biological replicates. The experiment included dye-swap, i.e. stressed fish were labelled red in two hybridisations and green in the other two hybridisations.

Common reference design [CGH_P. moluccensis and D. rerio]: four individual P. moluccensis gDNA samples are contrasted in four microarray hybridisations against a pooled gDNA sample consisting of three D. rerio. The experiment included dye-swaps.

middle: S

first: Julian

last: Caley

first: Alister

last: Ward

first: Ashley

middle: R

last: Connolly

first: Ross

middle: H

last: Crozier


title: Maf1 chromatin immunodepletion upon rapamycin treatment

city: Gif Sur Yvette

first: Michel

last: Werner

department: Biologie Joliot-Curie

institute: Commissariat à L'Energie Atomique-Saclay

summary:
Evidence of Maf1 recruitment to Pol III promoters during transcriptional repression induced by rapamycin
Keywords: Chromatin Immunodepletion on Chip time course

overall_design: Incubation of crosslinked chromatin with antibodies directed against the myc-tagged Maf1 resulted in a near complete depletion of Maf1 from the supernatant as observed by Western blot. We compared the DNA fragments associated with the crosslinked chromatin after and before Maf1 immunopurification by hybridization to intergenic DNA microarrays (depletion analysis)

first: Danuta

last: Oficjalska

first: Olivier

last: Harismendy

last: Lefebvre


title: Pol III transcription machinery occupancy monitoring upon rapamycin treatment

summary:
Effects of Maf1 deletion on the promoter occupancy during transcriptional repression by rapamycin
Keywords: ChIP-Chip time course

overall_design: Epitope tagged chromatin proteins, Brf1-13myc and  Bdp1-13myc (TFIIIB subunits), t95-13myc (TFIIIC subunit) and 3HA-C160 (Pol III subunit) were crosslinked to their targets in vivo. Cells were grown in rich YPD medium.  Protein-DNA interactions were fixed in exponential growth phase without treatment or after 30 min of treatment with rapamycin. Genome-wide analysis of the enrichment of DNA fragments, immunopurified with antibodies directed to epitope tags, was performed in triplicate in each case. Enrichment ratio in replicates samples were normalized to the GeneList1 (median = 1) representing loci not targeted by the Pol III transcription machinery according to a previous study (Harismendy et al. 2003).


title: Effect of a high fat diet on the hypothalami of mice susceptible to diet-induced obesity KOZAK2_ABI_HYP

status: Public on Apr 28 2006

city: Baton Rouge

first: Jessica

last: Hogan

state: LA

address: 6400 Perkins Rd.

department: Molecular Genetics

institute: Pennington Biomedical Research Center

summary:
The experimental goals of this study were to determine the differences in hypothalamus gene expression in genetically identical mice that have variability in their susceptibility towards diet-induced obesity following 6 weeks feeding a high fat diet, 2 weeks low fat diet and 6 weeks high fat diet.
Keywords: Comparative gene expression analysis

overall_design: Gene expression analyses was performed from pooled hypothalamus RNA from male C57BL/6J mice exhibiting high or low weight gain after 6 weeks feeding a high fat diet, 2 weeks low fat diet and 6 weeks high fat diet.  Four technical replicates were performed for each pool of RNA from high (H1, H2, H3, and H4) and low (L1, L2, L3, and L4) weight gaining mice.

first: Rob

last: Koza

first: Larissa

last: Nikonova

first: Jong

last: Rim

first: Tamra

last: Mendoza

first: Christopher

last: Faulk

first: Jihad

last: Skaf

first: Leslie

middle: P

last: Kozak


title: Rootstock-dependent gene expression profiling in apple scions

status: Public on May 05 2006

city: University Park

first: Izabela

last: Makalowska

state: PA

address: 502 Wartik Lab

institute: Pennsylvania State University

summary:
The purpose of this project is to examine the effects of rootstocks on the gene expression patterns in scions of  apple trees.  Gene expression patterns were examined in the Gala variety grafted onto seven different, commonly used rootstocks.  These trees were grown in the greenhouse to limit environmental effects.  Also, gene expression profiles were examined in three different varieties (Ambrosia, Melrose,and Gala) grafted onto B.9 rootstocks grown in the field.
Keywords: apple, rootstock, graft, scion

overall_design: Each sample is a pool of RNA from two different trees.  RNA samples were isolated from 0.5 g of actively growing shoot tips, including leaf and stem tissues.

first: Timothy

last: McNellis

first: Philip

middle: J

last: Jensen

first: Robert

middle: M

last: Crassweller

first: James

last: Travis

first: Naomi

last: Altman

first: Craig

last: Praul

first: Siela

last: Maximova

first: Qing

last: Zhang


title: Diet-induced obesity Kozak1_ABI_ING

middle: A.

department: Genomics Core Facility

summary:
The experimental goals of this study were to determine differences in adipose tissue gene expression in genetically identical mice that have variability in their susceptibility towards diet-induced obesity following 4 weeks feeding a high saturated fat diet.
Keywords: comparative gene expression analysis

overall_design: Gene expression analyses was performed from pooled inguinal fat RNA from male C57BL/6J mice exhibiting high or low weight gain after 4 weeks on a high saturated fat diet (D12331; Research Diets, New Brunswick, NJ). Mice were singly-housed at weaning and fed the high saturated diet starting at 8 weeks fo age. Three technical replicates were performed for each pool of RNA from high (H1, H2 and H3) and low (L1, L2 and L3) weight gaining mice.

first: Jessica

last: Hogan

first: Jong-Seop


title: Yeast Histone ChIP-chips_Evidence for nucleosome depletion at active regulatory regions genome-wide (Lee et al. 2004)

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

summary:
The identification of nuclease-hypersensitive sites in an active globin gene and in the 5' regions of fruit fly heat shock genes first suggested that chromatin changes accompany gene regulation in vivo. Here we present evidence that the basic repeating units of eukaryotic chromatin, nucleosomes, are depleted from active regulatory elements throughout the Saccharomyces cerevisiae genome in vivo. We found that during rapid mitotic growth, the level of nucleosome occupancy is inversely proportional to the transcriptional initiation rate at the promoter. We also observed a partial loss of histone H3 and H4 tetramers from the coding regions of the most heavily transcribed genes. Alterations in the global transcriptional program caused by heat shock or a change in carbon source resulted in an increased nucleosome occupancy at repressed promoters, and a decreased nucleosome occupancy at promoters that became active. Nuclease-hypersensitive sites occur in species from yeast to humans and result from chromatin perturbation. Given the conservation of sequence and function among components of both chromatin and the transcriptional machinery, nucleosome depletion at promoters may be a fundamental feature of eukaryotic transcriptional regulation.
Keywords: ChIP-chip

overall_design: Seven Myc-tagged H4 and four H3 ChIP-chip experiments were performed using input DNA as the reference. Results were compared to control experiments using input DNA, ChIPs lacking Myc epitope, or ChIPs without antibodies. Data from input vs. input control experiments are shown here. Also, four H3 ChIP-chip experiments were performed during heat shock. We loaded data into the University of North Carolina (UNC) Microarray Database. We normalized the ratios and retrieved the following ratio for each spot: log2 (median of ChIP pixel intensities/ median reference pixel intensities). Only spots of high quality by visual inspection, with gel-verified PCR products and comprised of pixels with consistent ratio values (regression correlation >0.6), were used for analysis.

first: Cheol

last: Lee

first: Yoichiro

last: Shibata

first: Bhargavi

last: Rao

first: Brian

last: Strahl


title: Mouse Atlas of Gene Expression Project

status: Public on Apr 27 2006

city: Vancouver

first: BCGSC

last: BC Cancer Agency

state: BC

address: 675 West 10th Avenue

department: Gene Expression

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

summary:
Mouse Atlas of Gene Expression Project
A Quantitative and Comprehensive Atlas of Gene Expression in Mouse Development.
Also available at CGAP: http://cgap.nci.nih.gov/
Keywords: LongSAGE, SAGE

overall_design: 191 LongSAGE libraries and 5 SAGE libraries


title: Prostate_5azadC

status: Public on May 08 2006

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

summary:
This microarray dataset accompanies the publication by Kim et al, "The retinoic acid synthesis gene ALDH1a2 is a candidate tumor suppressor in prostate cancer".  The dataset comprises four prostate cancer cell lines treated with the DNA methyltransferase inhibitor 5-aza-dC.  For each cell line, gene expression in treated (channel 2; Cy5) and untreated (channel 1; Cy3) cells is directly compared by hybridization to the same DNA microarray.  Further details on the treatment conditions are provided in the manuscript.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Keywords: compound_treatment_design

overall_design: Using regression correlation

first: Hanna

last: Kim


title: Mek inhibition, NOS inhibition, and nNOS knockout

status: Public on Apr 26 2006

city: Baltimore

first: Ted

last: Dawson

state: MD

address: 733 N. Broadway, MRB SUITE 731

department: Institute for Cell Engineering

institute: Johns Hopkins University School of Medicine

summary:
embryonic cortical neuron treated with CSS, NMDA and NMDA with Mek inhibitor:
replicate 1: GSM49556, GSM49557, GSM49558
replicate 2: GSM49559, GSM49560, GSM49561

nNOS KO brain cortex and wild-type littermate brain cortex:
GSM49562, GSM49563

embryonic cortical neuron treated with CSS, NMDA and NMDA with NOS inhibitor:
replicate 1: GSM49618, GSM49619, GSM49620
replicate 2: GSM49621, GSM49622, GSM49623
Keywords: other

sample_organism:
Mus musculus
Rattus norvegicus


title: Genes regulated by E47

status: Public on Apr 22 2006

first: Tomokatsu

last: Ikawa

address: 9500 Gilman Drive

department: Biology

institute: UCSD

summary:
To find the target genes regulated by E47 in hematopoietic progenitor cells
Keywords: genetic modification

overall_design: E2A-deficient hematopoietic progenitor cells were infected by E47ER or bHLHER. 48 hours later, the cells were induced by 4-hydroxytamoxifen for six hours.

first: Cornelis

last: Murre


title: clp1 induction

status: Public on Apr 25 2006

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

summary:
The clp1 gene is a b-dependent gene required for clamp formation during the biotrophic growth phase of U. maydis. The gene was induced by means of a fusion to the arabinose inducable crg1 promoter. To exclude effects from the b-mating type locus, the experiments were performed in strain JB1 carrying a deletion of the entire b-locus.
Keywords: gene induction

overall_design: Strains JB1 (control) and JB1-crgP::clp1 were grown for 2 h in arabinose containing medium (inducing conditions). Samples were taken from two biological replicates each.

first: Mario

last: Scherer


title: Rose bengal pretreatment

status: Public on Apr 20 2006

city: Berkeley

first: Heidi

middle: Kristine

last: Ledford

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

summary:
Photoautotrophically grown wild type Chlamydomonas reinhardtii cultures were either "treated" with 2uM rose bengal at 50 umol photons m-2 s-1 or "untreated" with the same volume of water at the same light intensity.

The purpose is to identify genes that are regulated by singlet oxygen.
Keywords: stress response

overall_design:
Microarray slides were printed as part of the C. reinhardtii Genome Project (Im et al., 2002; Shrager et al., 2003; Zhang et al., 2004). Fragments corresponding to the last 400 bp at the 3’ ends of 2761 C. reinhardtii cDNAs were amplified and spotted onto polyamine-coated slides (Corning, Acton, MA). Each slide contained four replicate spots arrayed in four distinct grids. A total of 4 slides were used, encompassing two biological replicates, each with a dye switch control.

Slides GSM105771 and GSM105772 used the same biological samples, but with a dye switch. Slides GSM105773 and GSM105774 used the same biological samples, but with a dye switch.

first: Krishna

last: Niyogi


title: ORNL Hr(Rh-R) mouse cutaneous array

status: Public on Apr 18 2006

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta University

summary:
These data is from 10 day-old Hr(Rh-R)/Hr(Rh-R) vs Hr(Rh-R)/+ mice. Mouse 15k microarray from the Center for Applied Genomics was used to survey the gene expression. The data was acquired with ImaGene and processed with GeneSight from BioDiscovery.
Keywords: Genetic mutants

overall_design: Three pairs of littermates from one liter, 10 day-old Hr(Rh-R)/Hr(Rh-R) vs Hr(Rh-R)/+ mice, were used for the hybridization. Dye-swapping was done for each pair of littermates.

first: Brynn

last: Voy


title: Transcript profiling in A. pleuropneumoniae under iron restriction

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

institute: Université de Montréal - Faculté de Médecine Vétérinaire

summary:
To better understand effects of iron starvation on A. pleuropneumoniae and to identify new potential vaccine targets, we conducted transcript profiling using a DNA microarray containing all 2025 ORFs of the genome of A. pleuropneumoniae serotype 5b strain L20.  Upon comparing growth of this pathogen in iron-sufficient versus iron-depleted medium, 210 genes were identified as being differentially expressed.  Some genes (92) were identified as being up-regulated; many have confirmed or putative roles in iron acquisition, such as the genes coding for two TonB energy-transducing proteins and the hemoglobin receptor HgbA.  Transcript profiling also led to identification of some new iron acquisition systems of A. pleuropneumoniae.
Keywords: stress respsonse

overall_design:
The bacteria was grown in BHI broth with or without 50 ug/ml EDDHA to generate iron restriction.  RNA extractions were performed on five different days using the QIAGEN RNeasy Kit, and a total of nine hybridization were performed, including three pairs of dye swap experiments and a pair of hybridizations being a direct repeat (same dyes).

Data were acquired using a Perkin-Elmer ScanArray Express scanner, and were quantified, normalized and analysed using the SpotFinder, MIDAS and TMEV software from TIGR's TM4 Suite of Microarray Analysis softwares.

first: John

last: Nash

first: Josée

last: Harel

first: James

last: Coulton

last: Jacques


title: Near Naked Hairless mouse skin array

summary:
This is the data from 7 day-old homozygous Hrn mutant mice compared to the wild type mice with mouse 22k compugen oligolibrary 2.0. The data was normalized with GeneSight from BioDiscovery and analyzed with SAM.
Keywords: Genetic mutant

overall_design: 7 day-old near naked hairless mutant mice vs 7 day-old wild type mice. Five biological replicates were used from one litter. Dye-swapping was done to remove dye-specific errors


title: ORNL 5wk Hr(n)/+ mice skin array

summary:
This array is spotted in house in order to survey the interested genes expressed mainly in skin with the selection of the clones from Research Genetics.
Keywords: Genetic Mutant

overall_design: 5 week-old heterozygous Hr(n) mutant mice vs wild-type mice was used in the microarray. Four biological replicates were included from the same litter. Dye swapping was done to control dye-specific errors. The data was analyzed with ImaGene and GeneSight from BioDiscovery.


title: Comparison of miRNA expression in Dickkopf1-expressing versus control newborn mouse skin

status: Public on May 04 2006

city: New York

first: Sarah

middle: E

last: Millar

state: NY

address: Icahn Building, Floor 13 Room 020C, 1425 Madison Ave

department: Developmental, Cell and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

summary:
miRNA expression was compared in skin from control newborn mice and littermate mice ectopically expressing the potent secreted WNT inhibitor Dickkopf 1 (DKK1) in the epidermis. DKK1 completely suppresses hair follicle development. Multiple miRNAs were identified that reproducibly produced signals above background in both types of skin sample. Several miRNAs were identified for which hybridization signals were on average more than 2.5 fold higher in control samples than in Dkk1-expressing samples, suggesting these may be upregulated in hair follicles, and/or are direct or indirect targets of WNT inhibition in the skin.
Keywords: miRNA expression array, transgenic mouse, skin, WNT

platform_organism:
Arabidopsis thaliana
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
Low molecular weight RNA was isolated using the mirVana RNA extraction kit (Ambion) from full thickness dorsal skin of three K5-rtTA; tetO-Dkk1 newborn mice and three control littermates following doxycycline treatment from E0.5 to induce expression of Dkk1 in double transgenic epidermis [1]. Control and Dkk1–expressing transgenic samples were tagged for labeling with Cy3 and Cy5 dyes respectively using the Ncode miRNA Labeling System (Invitrogen), mixed by equal mass, and co-hybridized to miRNA arrays that have been described previously [2]. Background-corrected median signals for pixels from each probe spot in both the Cy3 and Cy5 channels were used for analysis. Cy3 (control samples C2, C4, C5) was detected at 532nm and Cy5 (Dkk1–expressing transgenic samples TG1, TG2, TG4) at 635 nm.

References:
[1]	Chu, E.Y., Hens, J., Andl, T., Kairo, A., Yamaguchi, T.P., Brisken, C., Glick, A.,
 Wysolmerski, J.J., and Millar, S.E. (2004). Canonical WNT signaling promotes
 mammary placode development and is essential for initiation of mammary gland
 morphogenesis. Development 131, 4819-4829.

[2]	Nelson, P.T., Baldwin, D.A., Scearce, L.M., Oberholtzer, J.C., Tobias, J.W., and
 Mourelatos, Z. (2004). Microarray-based, high-throughput gene expression profiling of
 microRNAs. Nat Methods 1, 155-161.

first: Thomas

last: Andl

first: Elizabeth

last: Murchison

first: Fei

first: Yuhang

last: Zhang

first: Monica

last: Yunta-Gonzalez

last: Tobias

first: Claudia

middle: T

last: Seykora

first: Gregory

last: Hannon


title: Analysis of rap overexpression and phr deletion on gene expression in Bacillus subtilis

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

address: 31 Ames Street, 68-530

institute: MIT

summary:
We monitored changes in Bacillus subtilis global gene expression in response to overexpression of rapF, rapH, rapJ, or rapK or deletion of phrC, phrF, or phrK.
Keywords: genetic modifications

overall_design: For monitoring changes in gene expression in response to rap overexpression, we grew cells that contained an IPTG-inducible copy of rapF, rapH, rapJ, or rapK in S750 minimal media.  Treated and untreated cultures were grown in parallel.  At OD600 ~ 0.5, we added IPTG (1 mM final volume) to induced cultures. We collected samples from induced and uninduced cultures ~30 min. later.  We extracted RNA, reverse transcribed, labeled, and co-hybridized induced and uninduced samples to arrays containing PCR products amplified from >99% of B. subtilis genes.  We performed three independent replicates of each experiment.  For monitoring changes in gene expression in response to deletion of each phr, we grew wild-type and phrC, phrF, and phrK null cells in minimal media to OD600~1.  We collected samples and extracted RNA, reverse transcribed, labeled, and co-hybridized each RNA along with a labeled reference pool of RNAs to arrays containing 65-mer oligonucleotides complementary to  >99% of B. subtilis genes.  We performed three independent replicates of each experiment. For final analysis of these samples, we then made ratios of each phr null mutant to a paired wild-type sample.

first: Jennifer

last: Auchtung

first: Catherine

last: Lee


title: FVB nerve x SC comparison

status: Public on Apr 15 2006

city: Amsterdam

first: Anneloor

last: ten Asbroek

address: Meibergdreef 9

country: Netherlands

institute: Academic Medical Center

summary:
wild-type mouse (FVB strain) expression profiles of adult sciatic nerve and of cultured Schwann cell
Keywords: other

middle: L

first: Fred

last: van Ruissen

first: Jan

last: Ruijter

first: Frank

last: Baas


title: cDNA microarray analysis of human skeletal muscle after eccentric exercise

city: Ottawa

first: Douglas

middle: Joseph

last: Mahoney

state: ON

address: 401 Smyth Rd

department: Apoptosis Research Center

institute: CHEO Research Institute

summary:
We examined global mRNA expression using cDNA microarrays in skeletal muscle of humans before, and 3h and 48h after 300 maximal eccentric contractions.
Keywords: Time course

overall_design: Healthy, non-trained university-aged subjects performed 300 single leg maximal eccentric contractions. Skeletal muscle biopsies were taken from the vastus lateralis before, 3h and 48h after the exercise bout. Total RNA was extracted, amplified, reverse transcribed, and cDNA was analyzed on a custom made cDNA microarray. Four subjects were analyzed, and samples were not pooled between subjects (i.e. individual microarrays were used for baseline vs. 3H and baseline vs. 48h for EACH subject; repeated measures design).

first: Gianni

last: Parise

first: Simon

last: Melov

first: Adeel

last: Safdar

first: Minghua

last: Fu

first: Eric

last: Payne

first: Mark

middle: A

last: Tarnopolsky


title: D. nodosus WT vs pilR mutant

city: Melbourne

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

institute: Monash University

summary:
The aim was to determine the additional genes regulated by PilR in addition to fimA. To determine the additional genes the gene expression profile of a pilR mutant was compared to the wild-type strain.
Keywords: genetic modification

overall_design: PilR regulated genes were determined by analysed microarray expression data from three biololgical replicates, including a dye swap. The expression data from the pilR mutant was compared to the wild-type strain. Raw data was obtained using IMAGENE, while normalisation and analysis was performed using BASE. Statistical analysis was undertaken using the Wilcoxon signed rank test.

first: Dane

last: Parker

first: Ruth

last: Kennan

first: Gary

last: Myers

first: Ian

last: Paulsen


title: CornChip0-Maize Pilot GeneChip Array

status: Public on Apr 14 2006

city: Ames

first: Roger

last: Wise

state: IA

address: 411 Bessey Hall

institute: Iowa State University

summary:
To define the parameters necessary to design short oligo arrays for maize (Zea mays L.), a species with particularly high nucleotide (SNP) and insertion-deletion (indel) polymorphism frequencies, gene expression was analyzed in for four maize inbred lines using a custom Affymetrix DNA array. Statistically significant interactions between probes and maize inbreds were detected, affecting five or more probes (out of 30 probes per transcript) in the majority of cases, indicating the effect of polymorphisms on gene expresison estimates using this platform.
Keywords: genotype effect

overall_design: Plant growth, tissue collection and RNA extractions were repeated three times (biological replication) for each of four maize lines: B73, Mo17, W23 and Wf9. Total RNA was labeled according to the Affymetrix Expression Analysis Manual, and hybridized to two CornChips (technical replicates). A total of six replicates (three biological, two technical) of each line were hybridized to the CornChips.

first: Virginia

last: Walbot

first: Edward

middle: S

last: Buckler

first: Gene

last: Tanimoto

first: Matias

last: Kirst

first: Rico

last: Caldo

first: Paula

last: Casati


title: Comparison of cotton fiber to ovule at 9 DPA

status: Public on Apr 12 2006

city: Shanghai

first: Xiao-Ya

last: Chen

address: No. 300, Fenglin Road

department: Institute of Plant Physiology and Ecology

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
RNAs from the upland cotton 9-DPA fibers were compared to the 9-DPA fiber-detached ovule.
Keywords: tissue comparison

first: Jin-Ying

last: Gou

first: Ling-Jian

last: Wang


title: Comparison of upland li mutant with normal fibers

summary:
The G. hirsutum mutant li1 is caused by a dominant mutation which has pleiotropic effects on plant development. To get information for molecular effects by li1 mutation on cotton fiber development, we examined expression patterns of over 5000 genes by cDNA array from 6 to 18 DPA in a 3-day interval between li1 mutant and normal fibers.
Keywords: Mutant and normal fiber comparison

overall_design: RNAs from li1 mutant fibers at 6-, 9-, 12-, 15-, and 18-DPA were compared to normal fiber RNA at each corresponding time points. Four biological repeats were carried out including two dye-swap ones.


title: Gene Expression Profile Modified by TTT

status: Public on Apr 05 2006

city: Iruma

first: Keisuke

last: Mori

state: Saitama

address: 38 Morohongo, Moroyama

department: Department of Ophthalmology

country: Japan

institute: Saitama Medical University

summary:
To study gene expression changes in the rat retina and choroid following transpupillary thermotherapy (TTT) and to identify molecular mechanisms that may enhance treatment of choroidal neovascularization, complicating age-related macular degeneration.
Keywords: Expression level alteration in the rat retina and choroid after TTT

overall_design: In Brown Norway rats, one fundus was treated with an 810-nm diode laser while the contralateral fundus received no treatment. The mRNA was extracted and processed for cDNA microarray analysis.

first: Yoko

last: Ito

first: Mitsuteru

first: Hiroyasu

last: Takita

first: Shin

last: Yoneya

first: Gholam

last: Peyman

first: Peter

last: Gehlbach


title: D. nodosus WT vs rpoN mutant

first: Julian

last: Rood

summary:
To determine the genes in addition to fimA regulated by sigma 54 by analysing the gene expression profiles of an rpoN mutant compared to the D. nodosus wild-type strain.
Keywords: genetic modification

overall_design: RpoN regulated genes were determined by analysing four biological replicates, including two dye swaps. Raw data was compiled using IMAGENE. Normalisation and statistical analysis was undertaken using BASE. Statistics were performed using the Wilcoxon signed ranked test.

first: Dane

last: Parker

first: Ruth

last: Kennan

first: Gary

last: Myers

first: Ian

last: Paulsen


title: Gene expression during early Arabidopsis flower development

status: Public on Apr 10 2006

city: Pasadena

first: Frank

last: Wellmer

address: 1200 E. California Blvd.

department: Biology 156-29

institute: California Institute of Technology

summary:
This experiment describes gene expression during early Arabidopsis flower development. We used a 35S:AP1-GR ap1 cal line to induce synchronized flower development by specifically activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as at one-day intervals for the following five days. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome microarrays (Operon).
Keywords: time course

overall_design: Four sets of biologically independent tissue samples were collect 0,1,2,3,4, and 5 days after activation of the AP1-GR fusion protein. Samples of consecutive time points from each set were co-hybridized to micoarrays. Dyes used for labeling the RNA populations derived from the individual samples were switched in the replicate experiments to reduce dye-related artefacts.

first: Marcio

last: Alves-Ferreira

first: Annick

last: Dubois

first: JoseLuis

last: Riechmann

first: Elliot

last: Meyerowitz


title: Human ependymomas.

city: Heidelberg

last: Mendrzyk

institute: German Cancer Research Center (DKFZ)

type: Genome variation profiling by genome tiling array

summary:
Whole-genome screening of DNA-copy number changes by array-based or matrix comparative genomic hybridization (matrix-CGH).
Keywords: Repeat sample.

overall_design: Tumor DNA (Cy3) was hybridized against a single standard reference DNA-pool (Cy5) of the opposite sex than the patient.


title: Normal vs. Tumor Prostate miRNA

city: Research Triangle Park

first: Michael

last: Mattie

address: Five Moore Drive

department: Genomics Research

institute: GlaxoSmithKline

summary:
Comparison of miRNA expression profiles in a small set of prostate needle core biopsies or fine needle aspirates.
Keywords: Expression profiling of prostate needle core biopsies

overall_design:
MicroRNA expression was compared between a pooled normal sample consisting of 10 separate normal adjacent to tumor prostate needle core biopsies, two prostate tumor cell lines (PC3 and LNCaP), two needle core biopsies, and a fine needle aspirate of a prostate tumor metastasis to the supraclavicular lymph node.

MicroRNA was isolated from fresh frozen tissue sections of the needle core biopsies using the mirVana miRNA Isolation kit from Ambion per the manufacturer's instructions.  MicroRNA was amplified using 10 ng input and 750 ng of amplified material was subsequently labeled for hybridization.  All samples were normalized to the same normal prostate control.

first: Christopher

last: Haqq


title: PC3 vs LNCaP amplified and unamplified miRNA

summary:
Comparison of miRNA expression profiles directly comparing PC3 cells to LNCaP cells using unamplified and amplified miRNA.
Keywords: Expression profiling of hormone sensitive vs. insensitive prostate cancer cell lines and evaluation of amplification fidelity

overall_design:
MiRNA expression was compared between untreated PC3 (hormone insensitive) vs LNCaP (hormone sensitive) prostate cancer cell lines.  Six replicates were performed on enriched and unamplied miRNA from both cell lines.  Three replicates were performed on enriched and amplified miRNA from both cell lines.

Both cell lines were grown to ~70% confluency and harvested for enriched miRNAs using the mirVana Isolation kit from Ambion per manufacturer's instructions.  A total of 200 ng of enriched PC3 miRNA was labeled with Cy3 and LNCaP was labeled with Cy5 using the Array900 miRNA RT kit from Genisphere.

middle: C

last: Benz

middle: K

last: Scott

first: Robert

last: Getts

first: Vita

last: Fedele

first: Jessica

last: Bowers


title: Characterization of the ArsRS regulon of Helicobacter pylori

status: Public on Apr 01 2006

city: Wuerzburg

first: Dagmar

last: Beier

address: Am Hubland

institute: Universität Wuerzburg

summary:
The human gastric pathogen Helicobacter pylori is extremely well adapted to the highly acidic conditions encountered in the stomach. The pronounced acid resistance of H. pylori relies mainly on the ammonia-producing enzyme urease, however, urease-independent mechanisms are likely to contribute to acid adaptation. Acid-responsive gene regulation is mediated at least in part by the ArsRS two-component system consisting of the essential OmpR-like response regulator ArsR and the non-essential cognate histidine kinase ArsS whose autophosphorylation is triggered in response to low pH. In this study by global transcriptional profiling of an ArsS-deficient H. pylori mutant grown at pH 5.0 we define the ArsR~P- dependent regulon consisting of 110 genes including the urease gene cluster, the genes encoding the aliphatic amidases AmiE and AmiF and the rocF gene encoding arginase.
Keywords: Identification of an ArsRS-Regulon

overall_design:
Transcriptome analyses were performed using a whole-genome microarray containing 1649 PCR products generated with specific primer pairs derived from the genome sequences of H. pylori 26695 (Tomb et al., 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539-547) and J99 (Alm et al., 1999. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176-180) which were spotted in duplicate. Microarrays were produced as described by Gressmann et al. (Gressmann et al., 2005. Gain and loss of multiple genes during the evolution of Helicobacter pylori. PLoS Genet 1(4):e43). To determine genes which are differentially expressed in the ArsS-deficient mutant G27/HP165::km at pH 5.0, cDNA was prepared from RNA extracted from H. pylori G27 and G27/HP165::km after exposing the bacteria for one hour to acidic pH. A total of eight RNA samples from two independent RNA preparations from strain G27 and G27/HP165::km, respectively, was used for cDNA labelling und hybridisation. Dye reversal colour swaps were performed as follows: One cDNA sample was generated using Cy3-dCTP and the other using Cy5-dCTP resulting in four labelled cDNAs per colour swap. Cy5-dCTP and Cy3-dCTP labelled cDNAs were combined and hybridized to the H. pylori microarray. The slides were scanned using ScanArray HT and analysed by using the ScanArray express software (Perkin Elmer). Spots were flagged and eliminated from analysis when the signal to background ratio was less then three or in obvious instances of high background or stray fluorescent signals. Median intensities of spots were background corrected and differences in dye bias were normalized by using the LOWESS algorithm (Yang et al., 2002. Normalization for cDNA microarray data: a robuste composite method addressing single and multiple slide systematic variation. Nucleic Acid Res. 30:e15). The signal ratios as measure of differential expression between the red and green channels were obtained from processed signal intensities. Ratios were further analysed with Microsoft Excel (Microsoft) and SAM software for statistic significance (Tusher et al., 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98:5116-5121).
 	To determine the significance of differential expression RNA was isolated from the H. pylori G27 wild-type grown in BHI broth (pH 5.0), and 20 µg of this RNA were labelled either with Cy3-dCTP or with Cy5-dCTP. The two cDNA probes generated were hybridized onto the same slide, and the data were analysed as mentioned above. Signal ratios < 0.5 and > 2.0 were analyzed further.

last: Pflock

first: Nadja

last: Finsterer

first: Biju

last: Joseph

first: Hans

last: Mollenkopf

first: Thomas

middle: F

last: Meyer


title: Comparing effects of rapamycin and caffeine on gene expression in YPD media

status: Public on Apr 04 2006

city: Davis

first: Ted

last: Powers

address: One Shields Ave

department: Molecular and Cellular Biology

institute: UC Davis

summary:
To identify genes influenced by rapamycin and caffeine in strains W303a, S288c, and Sigma 2000
Keywords: Drug dose response

overall_design: Arrays compare W303a, S288c, and Sigma 2000 cells grown in YPD and either untreated or treated with different concentrations of rapamycin or caffeine


title: Breast tumor miRNA profiling

summary:
Comparison of miRNA expression profiles in breast tumors clinically annotated for ErbB2, ER, and PR expression, as well as additional parameters.
Keywords: Expression profiling of breast tumor biopsies

overall_design: MicroRNA was extracted from 500 ng of Trizol extracted total RNA from fresh frozen sections of breast tumor biopsies using the mirVana miRNA Isolation kit from Ambion.  10 ng of enriched miRNA was amplified using the SenseAmp Plus protocol for miRNA from Genisphere Inc.  500 ng of amplified miRNA was labeled using the Array900 miRNA RT kit from Genisphere and hybridized to custom miRNA microarrays.

first: Gary


title: Analysis of the transcriptional response to DNA damage and replication arrest

first: Alan

last: Grossman

summary:
Our results indicate that the transcriptional responses to HPUra, MMC, and UV are only partially overlapping. recA is the major transcriptional regulator under all of the tested conditions and LexA appears to directly repress expression of 63 genes in 26 operons, including the 18 operons previously identified as LexA targets.  MMC and HPUra treatments caused induction of an integrative and conjugative element (ICEBs1) and resident prophages (PBSX and SPß), which affected expression of many host genes.  Consistent with previous results, induction of these mobile elements required recA.  Induction of the phage appeared to require inactivation of LexA. Unrepaired UV damage and treatment with MMC also affected expression of some of the genes that are controlled by DnaA. Furthermore, MMC treatment caused an increase in origin proximal gene dosage
Keywords: time dependent DNA damage response

overall_design:
Exponentially growing cultures (in S750 defined minimal medium at 37C) were split into two and one half was treated with UV,MMC, or HPUra. Comparisons were made between the mock treated and untreated samples. All experiments were performed with three biological replicates. Data are presented for 60min after treatment.

For each experiment we compared treated sample vs reference on one array and untreated sample vs same reference RNA on another array. We then obtained ratio of the separate microarray Cy5/Cy3 ratios.

first: Alexi

last: Goranov

first: Elke

last: Kuester-Schoeck

first: Jade

last: Wang


title: Cotton Fiber Development Time-course Analysis

first: Xiao-Ya

last: Chen

summary:
 To get glance to the events of the fast elongation and second cell wall synthesis stages of developing cotton fiber cells, we examined expression patterns of over 5000 genes by cDNA array from 3 to 18 DPA in a 3-day interval.
Keywords: Time Course

overall_design: RNAs from the 3-, 6-, 9-, 12-, 15-, and 18-DPA fibers were compared to the 9-DPA fiber RNA for time-course analysis. Four biological repeats were carried out including two dye-swap ones.

first: Jin-Ying

last: Gou

first: Ling-Jian


title: Gene expression patterns induced by 5-Fluorouracil in breast cancer cell lines

status: Public on Apr 07 2006

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

summary:
We have compared the changes in cell cycle and cell death parameters induced by 2 different concentrations of 5-FU (IC50 and IC80) in the breast adenocarcinoma cell line MCF7. G1/S cell cycle arrest was associated with both concentrations, whereas cell death was mainly induced after IC80 5-FU. These changes were correlated with gene expression assessed by cDNA microarray analysis. Main findings included an overexpression of p53 target genes involved in cell cycle and apoptosis (CDKN1A/p21, TP53INP, TNFRSF6/FAS and BBC3/PUMA), and significant repression of Myc. High dose 5-FU also induced a higher regulation of the mitochondrial death genes APAF1, BAK1 and BCL2, and induction of genes of the ID family.
Keywords: Dose Response

overall_design: Time and dose-dependent changes in gene expression, induced by 5-Fluorouracil, in breast carcinoma cell lines MCF7, and MDA-MB-435.

first: Héctor

last: Hernández-Vargas

first: Pedro

last: Carmona-Saez

first: Gema

last: Moreno-Bueno

first: Jose

last: Palacios


title: Effect of caffeine on WT versus 3HA-TOR1 [I1954V + W2176R]

summary:
Comparing the effects of caffeine on cells expressing either WT 3HA-TOR1 or 3HA-TOR1 [I1954V + W2176R]
Keywords: Dose response in wild type versus mutant

overall_design: tor1 deletion cells in the W303a background were transformed with either p3HA-TOR1 or p3HA-TOR1 [I1954V + W2176R] and were treated with 0, 3, 6, and 9 mM caffeine.


title: Profiling of Dolphin Skin Cells

city: Charleston

first: MarineGenomics

last: Project

state: SC

address: 331 Fort Johnson Rd

summary:
3 technical replicates from Wild Dolphin PBL
Keywords: Immune and stress response analysis

overall_design: Analyzed 3 arrays with a 3 replicate series.

first: Annalaura

last: Mancia

first: Mats

last: Lundqvist

first: Tracy

last: Romano

first: Margie

last: Peden-Adams

first: Patricia

last: Fair

first: Mark

last: Kindy

first: Blake

last: Ellis

first: Sebastiano

last: Gattoni-Celli

first: David

middle: J

last: McKillen

first: Harold

last: Trent

first: Yian

first: Jonas

last: Almeida

first: Paul

last: Gross

first: Robert

middle: W

last: Chapman

first: Gregory

last: Warr


title: Bhh signaling in pronephric development

status: Public on Mar 31 2006

first: Curtis

middle: R

last: Altmann

address: 599 Lexington Avenue

institute: Goodwin Procter LLP

summary:
Pronephric explants were dissected in the presence or absence of hedgehog signaling.  Targets from pooled biological samples were examined in triplicate and the expression profiles were determined using Affymetrix Xenopus Genechip 1 arrays.
Keywords: repeat

overall_design: 3 bhh treated pooled explants and 3 untreated pooled explants were analyzed

first: Anna

last: Urban

first: Xiaolan

last: Zhou

first: Josette

middle: M

last: Ungos

last: Raible

first: Peter

last: Vize


title: CGR8 mouse embryonic stem cells time-course experiment 0 days old vs 3 days old , 0days old vs 10 days old

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary:
time-course experiment with embryoid bodies of CGR8 mouse embryonic stem cells ; in the whole time-series RNA from 0 days old embryoid bodies were hybridized against RNA from 3 days and 10 days old embryoid bodies
Keywords = embryoid bodies
Keywords = mouse
Keywords = time-course
Keywords = oligonucleotide array
Keywords: time-course

first: Chris

first: Agapios

last: Sachinidis

first: Juergen

last: Hescheler


title: Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. II

city: Zürich

first: Keith

last: Hoek

address: private

country: Switzerland

institute: Currently unaffilliated

summary:
Spotted oligonucleotide microarrays were used to assess global differential gene expression comparing normal human melanocytes with six independent melanoma cell strains from advanced lesions. The data, validated at the protein level for selected genes, confirmed the overexpression in melanoma cells relative to normal melanocytes of several genes in the growth factor/receptor family that confer growth advantage and metastasis. In addition, novel pathways and patterns of associated expression in melanoma cells not reported before emerged.
Keywords: class comparison study (melanoma vs melanocyte)

overall_design: Six melanoma cultures and two melanocyte cultures. The melanoma cultures are considered, for the purposes of this investigation, replicates from the point of view that they are all melanomas.  Three of the melanomas were replicated once or twice in addition.

last: Rimm

first: Kenneth

last: Williams

first: Hongyu

last: Zhao

first: Stephan

last: Ariyan

first: Aiping

last: Lin

first: Harriet

last: Kluger

first: Aaron

last: Berger

first: Elaine

last: Cheng

first: Sergio

last: Trombetta

first: Terence

last: Wu

first: Michio

last: Niinobe

first: Kazuaki

last: Yoshikawa

last: Hannigan

first: Ruth

last: Halaban


title: reversible and irreversible Thy-1 nephritis

city: Tokyo

first: Toshiaki

last: Monkawa

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Internal Medicine

institute: Keio University School of Medicine

summary:
To identify genes that play an important role in the irreversible progression of renal injury, we used microarray technology to identify differences in gene expression between these models.
Keywords: time course

overall_design: Rats were intravenously injected with mAb 1-22-3 one week after unilateral nephrectomy (irreversible model) or a sham operation (reversible model), and rats were sacrificed on day 4, 7, 14, 42, and 56 after the injection. cDNA probes prepared from kidney mRNAs were hybridized with oligonucleotide microarrays containing 4854 rat genes.


title: Adult male Fundulus heteroclitus exposed to Cr(VI)

city: Ocean Springs

first: Jonathan

last: Roling

state: MS

address: 703 East Beach Dr

department: Department of Coastal Sciences

institute: University of Southern Mississippi

summary:
Cr(VI) is a common bioavailable toxic metal that can cause oxidative stress, DNA adducts, and perturb normal gene expression.  Changes in gene expression are useful biomarkers of toxicant exposure that provide information about the health of an organism, its ability to adapt to its environment, and indicate potential toxicant-specific effects.  Therefore, we developed a toxicology array to the estuarine sentinel species Fundulus heteroclitus, or mummichog.
Adults males were exposed to Cr(VI) for 7-days at 0, 1.5 (NOEC), or 3 mg/L (LOEC).  Livers were excised and RNA isolated.  Adults are used in the laboratory experiments so that we can compare laboratory studies to fish caught at chromium-contaminated field sites.  Cr(VI) altered the expression of 12 genes in adult liver, including hepatic growth factor activator, heart fatty acid binding protein, and complement component C3-2.
Keywords: dose response

platform_organism:
Fundulus heteroclitus
Pseudopleuronectes americanus

overall_design: Adult male mummichogs were exposed to potassium chromate at either 0, 1.5 (0.0288 mM), or 3 mg/L (0.0577 mM) Cr(VI) for 7-days.  Each treatment group had 6 individually exposed fish in 3.8L plastic containers with static renewals every 48 hours.  Mummichogs were housed at 25C in a 14/10 light/dark cycle at 18‰ salinity.  At the conclusion of the exposures, livers were excised and placed in TRI-Reagent® for RNA isolation (Sigma Chemical Co, St. Louis, MO), and stored at -80C.

first: William

last: Baldwin


title: Glioma

first: Tokuzo

last: Arao

address: Tsukiji 5-1-1, Chuo-ku

department: Shien lab

institute: National Cancer Center Hospital

summary:
Mean age of patients was 53.2 years old (range, 18–80). Twenty-two patients were males, and 7 were females. Tissues were snap-frozen in liquid nitrogen within 5 min of harvesting, and stored thereafter at －80℃. Samples were specifically re-reviewed by a board-certified pathologist in our institution, using observation of sections of paraffin-embedded tissues that were adjacent or in close proximity to the frozen sample from which the RNA was extracted.
Keywords: disease state analysis

overall_design: grade III and IV glioma and survival time

first: Ryuya

last: Yamanaka

first: Kazuto

last: Nishio


title: Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila

city: Amsterdam

first: Maarten

last: van Lohuizen

address: Plesmanlaan 121

department: Molecular Genetics

institute: NKI-AVL

type: Genome binding/occupancy profiling by array

summary:
Polycomb group (PcG) proteins maintain transcriptional repression of developmentally important genes and have been implicated in cell proliferation and stem-cell self-renewal. We used a genome-wide approach to map binding patterns of PcG proteins (Pc, esc and Sce) in Drosophila Kc cells. We found that Pc associates with large genomic regions of up to ~150kb in size, hereafter referred to as “Pc-domains”. Sce and esc accompany Pc in most of these domains. PcG-bound chromatin is trimethylated at histone H3 lysine 27 and in general transcriptionally silent. Furthermore, PcG proteins preferentially bind to developmental genes. Many of these encode transcriptional regulators and key components of signal transduction pathways, including Wingless, Hedgehog, Notch and Delta. We also identify several new putative functions of PcG proteins, such as in steroid hormone biosynthesis. These results highlight the extensive involvement of PcG proteins in the coordination of development through the formation of large repressive chromatin domains.
Keywords: DamID, Chromatin immunoprecipitation, ChIP-chip

overall_design:
To study PcG binding profiles we used DamID, which is based on the ability of a chromatin protein fused to E.coli DNA adenine methyltransferase (Dam) to methylate the native binding site of the chromatin protein. Dam-fusion proteins are expressed at very low levels to avoid mistargeting. Subsequently, methylated DNA fragments are isolated, labeled and hybridized to a microarray. Methylated DNA fragments from cells transfected with Dam alone served as reference. Genomic binding sites of the protein can then be identified based on the targeted methylation pattern.
For detailed background information on DamID, see: van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 27, 304-8 (2001); van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8 (2000).

first: Bas

last: Tolhuis

first: Inhua

last: Muijrers

first: Elzo

last: de Wit

first: Hans

last: Teunissen

first: Wendy

last: Talhout

last: van Steensel


title: Juvenile Fundulus heteroclitus exposed to Cr(VI)

summary:
Cr(VI) is a common bioavailable toxic metal that can cause oxidative stress, DNA adducts, and perturb normal gene expression.  Changes in gene expression are useful biomarkers of toxicant exposure that provide information about the health of an organism, its ability to adapt to its environment, and indicate potential toxicant-specific effects.  Therefore, we developed a toxicology array to the estuarine sentinel species Fundulus heteroclitus, or mummichog.  Juvenile mummichog were exposed to potassium dichromate for thirty days at concentrations from 0 to 24 mg/L of Cr(VI), and growth was measured to determine the NOEC (1.5 mg/L or 0.0288 mM) and LOEC (3 mg/L or 0.0577 mM).  Body burdens from Cr(VI) exposed fish demonstrated a dose dependent increase and were inversely correlated to body weight.  Cr(VI)-exposed juvenile mummichog differentially expressed greater than 20 genes in a dose-dependent manner, including hepatic glucose transporter 2, liver fatty acid binding protein, ATPase synthase 8, type II keratin, TBT binding protein, and complement component C3-2.  Many of these genes are involved in energy metabolism or growth, which is consistent with the reduced growth caused by Cr(VI).
Keywords: dose response

overall_design: Juvenile mummichogs (Fundulus heteroclitus) were exposed to potassium chromate at either 0, 1.5 (0.0288 mM), or 3 mg/L (0.0577 mM) Cr(VI).  Thirty day exposures began within 48 hours of mummichog hatching.  Each treatment group had four 500mL plastic tanks with 6 fish per tank with static media renewals every 48 hours.  Mummichogs were housed at 25C in a 14/10 light/dark cycle at 18‰ salinity.  At the end of the exposure, half of the fish from each tank were euthanized and whole bodies were placed in TRI-Reagent® for RNA isolation (Sigma Chemical Co, St. Louis, MO), then stored at -80C.  The other three fish in each tank were used for chromium body burden determination.


title: Gene expression analysis of immune privileged site-associated DLBCL: The effect of HLA class II downregulation

city: Groningen

first: Marije

last: Booman

department: Pathology

institute: University Medical Center Groningen

summary:
Loss of human leukocyte antigen (HLA) expression on tumor cells is frequent in diffuse large B cell lymphoma (DLBCL) arising in immune-privileged sites such as the testis and central nervous system and is associated with small homozygous deletions of HLA-DQ/DR and larger hemizygous deletions of the major histocompatibility complex (MHC) region. To better understand the significance of downregulation of HLA class II expression in relation to the homozygous and hemizygous deletions, we analyzed global gene expression patterns in a series of 26 testicular diffuse large B-cell lymphomas (DLBCL) after characterization of these deletions. Low levels of HLA-DR mRNA in whole testicular DLBCL samples were associated with a strong downregulation of numerous immune-related genes specific for T-cells, macrophages, antigen presentation and processing, lymphocyte activation, chemokines and chemokine receptors and the complement system. Interestingly, hemizygous and homozygous deletions in the MHC region did not have any additional impact on global gene expression.
Keywords: Gene expression

overall_design:
Twenty-six primary testicular DLBCL and 10 primary nodal DLBCL were analyzed using an 18k cDNA microarray. Gene expression profiles were compared between several subsets:

- testicular vs nodal DLBCL

- testicular DLBCL with and without deletions

- testicular DLBCL with normal/high and low HLA-DR mRNA expression levels

first: Jenny

last: Douwes

first: Annuska

last: Glas

first: Sietske

last: Riemersma

first: Ekaterina

last: Jordanova

first: Klaas

last: Kok

first: Andreas

last: Rosenwald

first: Daphne

last: de Jong

first: Ed

last: Schuuring

first: Philip

last: Kluin


title: Expression patterns in stress conditions of 4 closely related yeast species from the Saccharomyces sensu stricto complex

city: Rehovot

first: Naama

last: Barkai

address: Hertzel

country: Israel

institute: The Weizmann Institute of Science

summary:
We characterize the genome-wide transcription response of four related yeast species and two strains to equivalent environmental stresses.
Keywords: Comparative analysis of gene expression across species.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus
Saccharomyces kudriavzevii
Saccharomyces mikatae

overall_design: We chose four yeast species, three species are represented by a single strain (S. cerevisiae, S. kudriavzevii and S. mikatae) and one species (S. paradoxus) is represented by two strains. The five different cell types were subjected to five environmental stresses: heat shock, oxidative stress (H2O2), growth on glycerol, nitrogen starvation and DNA damage (MMS). In each experiment, cells were grown to mid log-phase in rich media and were then subjected to the particular stress. The same growth media was used for all species. The genome-wide transcription profile of each culture was measured at six subsequent time points, from 10 to 90 minutes after the onset of the perturbation (one day for nitrogen starvation). At each time point, gene expression levels were measured relative to a reference (same culture before transfer to stressful media).

first: Adina

last: Weinberger

first: Itay

last: Tirosh


title: Sequence specific recognition of RNA hairpins by the SAM domain of Vts1

status: Public on Mar 24 2006

city: Toronto

first: Tzvi

last: Aviv

state: Ontario

address: 600 University

institute: Lunenfeld institute

summary:
Identifying transcripts that are associated with the post transcriptional regulator Vts1 in yeast by co-immuno precipitation.
Keywords: RNA pulldown, Co-IP

overall_design: Vts1-FLAG was overexpressed in vts1 deleted yeast cells, co-immuno precipitated and microarray probed together with cDNA from total RNA to detrmine ratio of enrichments by Vts1 pull downs.

first: Zhen

last: Lin

first: Giora

last: Ben-Ari

first: Craig

last: Smibert

first: Frank

last: Sicheri


title: Polysomal redistribution of mRNAs during restimulation of primed Th2 cells

status: Public on Mar 23 2006

city: San Francisco

first: Agnes

last: Paquet

state: CA

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

summary:
DO11.10 x TCR-Calpha-/- T cells stimulated under Th2 conditions for 6 days were centrifuged over Histopaque 1083 (Sigma) to remove dead cells, washed and rested for 20 min at 37C in complete media with 0.1 mg/ml cycloheximide (CHX, Sigma) added for the final 10 min.  Restimulated cells were activated with 10 ug/ml plate-bound I-Ad/ova complexes for 3 hrs. Cells were washed with ice-cold PBS/CHX and resuspended in polysome extraction buffer [30 mM HEPES (pH 7.4), 15 mM MgCl2, 0.3 M NaCl, 1% Triton X-100, 0.1 mg/ml CHX, 1 mg/ml heparin, 500 U/ml SUPERase-In RNAse inhibitors (Ambion, Austin, TX), 1x Complete EDTA-free protease inhibitor cocktail (Roche, Indianapolis, IN)].  After incubation on ice for 25 min, nuclei and debris were removed by centrifuging and the cleared supernatants transferred to fresh tubes.  1.5 ml of each extract (from 3 x 10exp8 T cells) were layered on a 37.5 ml 10-50% sucrose gradient prepared in SW28 ultraclear centrifuge tubes (Beckman Coulter, Fullerton, CA) using the salts described above, but without detergent, RNAsin or protease inhibitors. After centrifugation for 220 min at 28,000 rpm (average RCF = 103,745), fractions were isolated using an ISCO density gradient fractionator (Lincoln, NE) by pumping 60% sucrose into the bottom of the tube and collecting the displaced volumes into acid phenol:chloroform, with constant monitoring of ultraviolet absorbance at 254 nm.  Extracted RNA was precipitated with isopropanol, washed and resuspended in distilled water.  RNA from polysome associated fractions 7-12 of the gradients described above were pooled and 30-100 ug of total RNA per sample were used to template a Superscript III reverse transcription reaction (Invitrogen, Carlsbad, CA) incorporating amino-allyl dUTP (Sigma).  cDNA samples were washed with distilled water on microcon-30 columns (Millipore, Billerica, MA), dried and labeled with Cy3 (primed samples) or Cy5 (restimulated samples)  using CyDye reactive dye labeling kits (Amersham).  Unincorporated dye was removed using QiaQuick PCR purification columns (Qiagen), labeled cDNAs were eluted in 10mM Tris, pH 8, combined and dried. Fluorescence in the Cy3 and Cy5 channels was acquired using an Axon 4000B microarray scanner and GenePix software (Axon Instruments, Union City, CA). Data were normalized using the R package Bioconductor software and lowess normalization on the pixel medians without background subtraction (Ihaka and Gentleman, 1996).

Keywords = Th2 differentiation
Keywords = translation
Keywords = polysome profile
Keywords: cell stimulation

overall_design: This experiment is composed of two arrays, treated cells vs. primary cells.

first: Stefanie

last: Scheu

first: Daniel

middle: B

last: Stetson

first: Richard

last: Locksley


title: Comparative analysis of BCR-ABL tyrosine kinase inhibitors in BCR-ABL positive K562 cells

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

institute: Tokyo Medical University

summary:
Tyrosine kinase activity is the crucial enzymatic activity driving all known functions of the BCR-ABL protein and is required for protection from apoptosis by BCR-ABL, therefore, targeting this enzyme is an effective approach for therapeutic strategies. Recently, a novel structural entity, imatinib (STI571; Novartis, Basel, Switzerland), a potent and selective inhibitor of the tyrosine kinase activity of BCR-ABL, has shown promise against Ph-positive leukemia in human clinical trials. However, the emergence of imatinib resistance in patients with acute forms of Ph-positive leukemia has highlighted the need for overriding chemotherapy to eradicate this disease.
AMN107 and BMS-354825 are clinically active “next-generation” BCR-ABL inhibitors.
One potentially powerful approach is to use these compounds in combination with imatinib.
The rationale for such approaches is that an inhibitor cocktail may target the widest range of resistant clones and thereby delay the onset of acquired drug resistance.   More potent BCR-ABL inhibitors would be to target residual leukemia that persists in patients in whom imatinib induces durable remission but failed to eradicate the disease. From these points, our studies are performed to determine
(1) the differences of molecular signaling pathways between BMS-354825 and imatinib
(2) the mechanisms by which drug resistance of  BMS-354825 and imatinib occur except for point mutation of BCR-ABL kinase domain.
Keywords: drug sensitivity

overall_design:
(1)Comparison of gene expression patterens in K562 cells treated with tyrosine kinase inhibitors. For dual color analysis, K562 (MOC) was utilized as a reference.(i.e., Imatinib treated K562 cells vs BMS -354825 treated K562 cells vs Imatinib + BMS treated K562 cells).
(2) Compatrison of gene expression patterens between parental K562 cells and those in drug-resistant clones (i.e., K562-IMR and K562-BMSR).

first: Tetsuzo

last: Tauchi

first: Kousuke

last: Nunoda

first: Kazuma


title: Gene expression during pollen germination in Lily

city: Siena

first: Cecilia

last: Del Casino

address: Via Mattioli 4

department: Scienze Ambientali "G.Sarfatti"

country: Italy

institute: Università di Siena

summary:
cDNA microarray analysis of gene expression changes during pollen germination and tube growth in Lilium longiflorum L.
Keywords: other

first: Antonella

last: Autino


title: Macaca mulatta spleen sample exposed to SHIV 89.6 strain

status: Public on Mar 29 2006

city: Silver Spring

first: Rasha

last: Hammamieh

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

summary:
Splenic tissue was isolated from four adult male Indian-origin Rhesus monkeys serologically positive for non-pathogenic SHIV 89.6 and from matched uninfected four adult male Indian-origin Rhesus monkeys respectively. The corresponding RNA was processed by cDNA microarray analysis.

Keywords: SIV infection

overall_design: Sample RNA extracted from the tissue samples. Reference RNA was prepared from a pool of Rhesus monkeys' RNA. Microarray hybridization was carried out by labeling Reference RNA as Cy3 and sample RNA as Cy5. The sample was incubated at 55C for 16hr.


title: OCI-Ly3 CARD11 shRNA

status: Public on Mar 30 2006

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary:
Activation of NFkB pathway by CARD11
Keywords: time series design

overall_design: Cy3-labelled untreated sample and Cy5-labelled treated sample were hybridized to a Lymphochip microarray.


title: Breast Cancer experiments

summary:
Experimental studies confirmed n-6 type polyunsaturated fatty acid as pro-carcinogenic factor and n-3 fatty acid as cancer restraining agent; though their mode of action on tumor cells are still unclear.
Keywords: Time course

overall_design: To review the contrasting effect of omega-3 and omega-6 fatty acids over carcinoma by studying genomic alteration in treated cancer cells, two members from each family of PUFAs, namely EPA and DHA from n-3 PUFA family and, AA and LA from n-6 PUFA family was selected to treat four breast cancer cell lines: MDA-MB231, MDA-MB435S, HCC2218 and MCF-7 for two time period- 6hr and 24hr.


city: Koganei

first: Tadashi

last: Matsunaga

state: Tokyo

department: Biotechnology

institute: Tokyo University of Agriculture and Technology

summary:
Deatails of the series are available in the publications Suzuki et al., The Journal of Bacteriology “Global gene expression analysis of iron-inducible genes in Magnetospirillum magneticum AMB-1”, accepted for the publication. The gene expression profiles were categorized into 5 patterns. Abstract of the publication: "feo, tpd and ftr which encode ferrous transporters were up-regulated under iron-rich conditions.The concomitant rapid iron uptake and magnetite formation suggest that these uptake systems serve as iron supply lines for magnetosome synthesis."
Keywords: iron response

first: Takeyuki

last: SUZUKI

first: Yoshiko

last: OKAMURA

first: Calugay

last: RONIE

first: Haruko

last: TAKEYAMA

last: MATSUNAGA


title: Early gene expression responses to a Salmonella infection in the chicken intestine

city: Lelystad

first: Saskia

middle: van

last: Hemert

address: PO box 65

institute: Animal Sciences Group

summary:
1-day old chickens were orally inoculated with 1e5 c.f.u. Salmonella enteritidis. 24 hours after infection RNA from the jejunum was analysed. Two different microarray platforms were used, a homemade cDNA microarray and the Affymetrix GeneChip Chicken Genome Array
Keywords: host response; genetic background

overall_design:
There were 4 groups, 5 animals each. The microarray hybridisations were performed with pooled RNA samples.
4 comparisions were done:
-control fast growing chicken line vs. salmonella fast growing chicken line
-control slow growing chicken line vs. salmonella slow growing chicken line
-control fast growing chicken line vs. control slow growing chicken line
-salmonella fast growing chicken line vs. salmonella slow growing chicken line

last: van Hemert

first: Arjan

last: Hoekman

first: Mari

last: Smits

first: Johanna

last: Rebel


title: pH Regulates Genes for Flagellar Motility, Catabolism, and Oxidative Stress in Escherichia coli K-12

city: Gambier

first: Joan

middle: Lyn

last: Slonczewski

state: OH

address: 202 N. College Rd

department: Biology Dept

institute: Kenyon College

summary:
Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH. Cultures were grown with aeration to an optical density at 600 nm of 0.3 in potassium-modified Luria-Bertani medium buffered at pH 5.0, 7.0, and 8.7. For each of the three pH conditions, cDNA from RNA of five independent cultures was hybridized to Affymetrix E. coli arrays. Analysis of variance with a significance level of 0.001 resulted in 98% power to detect genes showing a twofold difference in expression. Normalized expression indices were calculated for each gene and intergenic region (IG). Differential expression among the three pH classes was observed for 763 genes and 353 IGs. Hierarchical clustering yielded six well-defined clusters of pH profiles, designated Acid High (highest expression at pH 5.0), Acid Low (lowest expression at pH 5.0), Base High (highest at pH 8.7), Base Low (lowest at pH 8.7), Neutral High (highest at pH 7.0, lower in acid or base), and Neutral Low (lowest at pH 7.0, higher at both pH extremes). Flagellar and chemotaxis genes were repressed at pH 8.7 (Base Low cluster), where the cell's transmembrane proton potential is diminished by the maintenance of an inverted pH gradient. High pH also repressed the proton pumps cytochrome o (cyo) and NADH dehydrogenases I and II. By contrast, the proton-importing ATP synthase F1Fo and the microaerophilic cytochrome d (cyd), which minimizes proton export, were induced at pH 8.7. These observations are consistent with a model in which high pH represses synthesis of flagella, which expend proton motive force, while stepping up electron transport and ATPase components that keep protons inside the cell. Acid-induced genes, on the other hand, were coinduced by conditions associated with increased metabolic rate, such as oxidative stress. All six pH-dependent clusters included envelope and periplasmic proteins, which directly experience external pH. Overall, this study showed that (i) low pH accelerates acid consumption and proton export, while coinducing oxidative stress and heat shock regulons; (ii) high pH accelerates proton import, while repressing the energy-expensive flagellar and chemotaxis regulons; and (iii) pH differentially regulates a large number of periplasmic and envelope proteins.
Keywords: Steady State

overall_design: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH. Overnight cultures were diluted 1:1000 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.0, pH 7.0, and pH 8.7. Bacteria were cultured in baffled flasks (less than 10% volume filled) with rotation at 240 rpm, incubated at 37°C to an optical density at 600 nm of 0.3. For each of the three pH conditions, RNA was isolated from five independent cultures.  Labeled cDNA was hybridized to Affymetrix antisense arrays according to standard procedures.  To analyze the expression levels, Dchip software was used to generate model-based expression indices normalized to sample pH 7 replicate 1.  ANOVA was used to identify genes with sitnificant expression differences among the three pH classes (p = 0.001).  For genes showing significant differences, the Log2 expression ratios were determined for each pair of pH classes, and significance was determined by Tukey's test (p = 0.001).

first: Lisa

last: Maurer

first: Elizabeth

last: Yohannes

first: Sandra

last: Bondurant

first: Michael

last: Radmacher

middle: L


title: Bovine tissue gene expression profiling at peak lactation

status: Public on Mar 21 2006

city: Urbana

first: Juan

middle: J.

last: Loor

state: IL

address: 1207 West Gregory Drive

department: Animal Sciences

institute: University of Illinois

summary:
Tissue from mammary, liver, and three adipose depots (mesenteric, omental, and subcutaneous) was collected at slaughter from a cow at peak lactation to examine gene expression profiles of 7872 sequences using a bovine cDNA microarray.
Keywords: comparative tissue gene expression

overall_design: RNA (20 ug) from tissues and a reference standard derived from a mixture of tissues were used to make aminoallyl-labeled cDNA followed by incorporation of Cy3-ester and Cy5-ester (Amersham, Piscataway, NJ).  Each experimental sample was co-hybridized with the reference standard, which allowed the treatment of fluorescence ratios as measurements of relative expression across all samples and time points.  Probes were hybridized to the array for 2 days at 42 C.  All samples were hybridized to duplicate slides for a total of 4 spots per cDNA element.  The microarray platform has already been described [Everts et al. (2005) Vet. Immunol. Immunopathol. 105:235-245].  Slides were scanned for both dye channels with a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).

first: Nicole

middle: A

last: Janovick Guretzky

first: James

last: Drackley

first: Robin

middle: E

last: Everts

last: Rodriguez-Zas

first: Harris

last: Lewin


title: SE challenged in 3 genetic chicken lines

status: Public on Apr 23 2006

city: Ames

first: Susan

last: Lamont

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

summary:
3 genetic chicken lines (Leghorn G-B1, Fayoumi, broiler) were used. chicken were challenged with SE at day 1, spleen and cecum tissues were collected at 2 hours and 16 hours after post challenge
Keywords: time-course

first: Huaijun

last: Zhou

first: Dan

last: Nettleton