title: Application of Serial Analysis of Gene Expression to the study of the gene expression profile of Leishmania infantum chagasi promastigote

status: Public on Aug 10 2011

city: TERESINA

first: ADELINO

middle: SOARES

last: LIMA NETO

state: PIAUI

address: RUA GOV. ARTUR DE VASCONCELOS, 151 CENTRO SUL

department: LEISHMANIOSES

country: Brazil

institute: INSTITUTO DE DOENÇAS TROPICAIS NATAN PORTELLA

summary: This study describes the application of the LongSAGE methodology to study the gene expression profile in Leishmania infantum chagasi. A tag library was created using the LongSAGE method and consisted of 14,208 tags of 17 bases. Of these, 8,427 (59.3%) were distinct. BLAST research of the 1,645 most abundant tags showed that 12.8% of them identified the coding sequences of genes, while 82% (1,349/1,645) identified one or more genomic sequences that did not correspond with open reading frames. Only 5.2% (84/1,645) of the tags were not aligned to any position in the L. infantum genome. The UTR size of Leishmania and the lack of CATG sites in some transcripts were decisive for the generation of tags in these regions. LongSAGE revealed the gene expression profile in promastigotes of L. i. chagasi. Additional analysis will allow a better understanding of the expression profile and discovering the key genes in this life cycle.

overall_design: The I-SAGETM Long kit (Invitrogen) was used to construct the L. i. chagasi library according to the manufacturer's recommendations. The following were included among the main steps: polyadenylates mRNAs were captured by oligo (dT) linked to magnetic beads and used for cDNA synthesis. The cDNA was digested with 60 U of NlaIII (anchoring enzyme) and the 3' ends of the cDNAs were isolated using the beads. The resulting cDNA 3' was divided into two equal portions and connected to two LongSAGE adapters, A and B. The long tags were released by the enzyme MmeI and linked to form ~130 bp ditags. Dilutions of 1:40 of the product were amplified in 27 PCR cycles (300 reactions in total). The precipitated PCR products were separated on 12% polyacrylamide gel and the 130 bp bands were cut out and the precipitated DNA was digested with NlaIII. The digestion products were separated on 12% polyacrylamide gel and ~34 bp ditags were cut out and linked to form concatemers. The concatemers were separated on 6% polyacrylamide gel and the fractions of 250-500 and 500-800pb were isolated and cloned into pZErO-1 vector digested with SphI. Vectors with concatemers were cloned in E. coli DH10b by electroporation and the isolated recombinant vectors were used as template for sequencing in the ABI Prism 3100 (Applied Biosystems).

first: OSVALDO

last: MELO NETO

first: CARLOS

last: COSTA


title: Expression analysis of the singlet oxygen resistant 1 (sor1) mutant

status: Public on Jul 15 2011

city: Dübendorf

first: Beat

middle: B

last: Fischer

address: Ueberlandstr. 133

department: Department of Environmental Toxicology

country: Switzerland

institute: Eawag

summary: In a screen for singlet oxygen resistant mutants, a mutant called sor1 was isolated with increased resistance to different oxidative and electrophilic stress conditions. This mutant was found to have a constitutive high expression of three known singlet oxygen response genes, a glutathione peroxidase GPX5 and two glutathione-S-transferase GSTS1 and GSTS2. The sor1 mutation was mapped to the gene of a 393-amino acid protein for which blast searches revealed only poor homology to other proteins but predicted a putative basic leucine zipper DNA binding domain indicating that it might function as transcription factor to activate gene expression during oxidative stress.Global expression analysis of sor1 compared to the untreated wild-type enabled to identify additional genes differentially regulated in the sor1 mutant including several other genes involved in oxidative stress response and detoxification of endogenous xenobiotics.

overall_design: The sor1 mutant and the corresponding wild-type strain 4A+ were grown mixotrophically in a Tris-acetate phosphate in three independent biological replicates. Then the cells of each replicate were harvested by centrifugation and total RNA was isolated using the RNeasy Mini Kit (Qiagen). DNA microarrays were performed using the ‘One-Color Microarray-Based Gene Expression Analysis’ system and a custom made 4 × 44 K ‘Chlamydomonas Whole Genome DNA Microarrays’ (Agilent Technologies) containing 15143 specific probes designed based on the Chlamydomonas version 4.0 transcript models provided by the DOE Joint Genome Institute (JGI), with an average of three replicates for each probe

first: Krishna

middle: K

last: Niyogi


title: Temporal changes in Listeria monocytogenes gene expression during salt stress

status: Public on Jul 01 2011

city: Ithaca

first: Teresa

middle: M

last: Bergholz

state: NY

address: 405 Stocking Hall

department: Food Science

country: USA

institute: Cornell University

summary: The foodborne pathogen Listeria monocytogenes experiences osmotic stress in many habitats, including foods and the gastrointestinal tract of the host.  While osmotic stress induced changes in expression have been investigated for specific genes, identifying and understanding genome-wide temporal changes in the transcriptome due to salt stress will provide insights into how this pathogen adapts to and survives this stress, leading to development of new intervention strategies.  To determine the short-term and long-term responses to salt stress, we exposed exponential phase cells of L. monocytogenes H7858 to 6% NaCl in Brain Heart Infusion (BHI) broth at 7°C and 37°C and extracted RNA after 2.5%, 5%, 10%, and 20% of lag phase and during exponential growth in BHI + 6% NaCl, and evaluated temporal changes in transcript levels with microarrays.  The temperature dependent short-term response to salt stress included a significant increase in transcript levels of the alternative sigma factor σB, with maximum expression at 2.5-5% of lag phase at 37°C, and at 20% of lag phase at 7°C.  Transcript levels of genes known to be regulated by σB, including inlAB, opuCA, glpFK, and gadBC, were significantly upregulated at the same relative time points as σB   As indicated by significantly elevated transcript levels during exponential growth in BHI + 6% NaCl, genes encoding proteins involved in purine and pyrimidine synthesis and amino acid biosynthesis are part of the long-term response to salt stress at 37°C.  Transcript levels of virulence genes plcA, mpl, actA, and plcB were also significantly upregulated during exponential growth under salt stress at 37°C.  Genes encoding proteins involved in protein degradation and stability and cell membrane modifications are part of the long-term response to salt stress at 7°C.  Overall, an initial alteration in the transcriptome occurs, decreasing transcript levels of genes encoding proteins involved in energy conversion and metabolism, while increasing transcript levels of those involved in the stress response controlled by σB, followed by a long-term response, including increased expression of genes encoding compatible solute transporters and general stress proteins, facilitating growth under salt stress.

overall_design: A reference design was used to analyze gene expression differences.  Exponential phase cultures at 37C and at 7C were used as a reference for salt stressed samples at each temperature.  Salt stressed samples from the same relative time point were compared across temperatures.  4 biological replicates were tested for each comparison.

first: Martin

last: Wiedmann

first: Kathryn

middle: J

last: Boor


title: functional characterization of vvmyb82-Functional characterization of the transcription factor VvMYB82

status: Public on Jul 06 2011

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

summary: ra07-05_myb82 - functional characterization of vvmyb82 - Functional characterization of the transcription factor VvMYB82 which is a regulator of the different phenolic compound biosynthesis.  - To compare wt with a surexpressor of VvMYB82 (Line A311 = 35s::VvMYB) and wt with a loss of function mutant AtMYB82

overall_design: 2 dye-swap - wt vs mutant comparison

first: Jean-Pierre

last: Renou

first: François

last: Barrieu

first: Thilia

last: Ferrier

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


status: Public on Jun 30 2011

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

summary: PEO1 is part of the PEO/PEA series of ovarian cancer cell lines established in 1988 from progressive samples from three separate cases of ovarian cancer (Langdon et al., 1988).

overall_design: Copy number profiling of PEO1 ovarian cancer cell line on Illumina HumanOmni1-Quad BeadChip

first: Susanna

last: Cooke

first: James

middle: D

last: Brenton


title: Transcript Profiling of Arcuate Nucleus in Response to Electroacupuncture on Rats

status: Public on Jul 07 2011

city: Shanghai

first: ke

last: wang

address: 151 Libing Road

country: China

institute: Shanghai Biochip Co., Ltd.

summary: The electroacupuncture-induced analgesic effect has been used widely to alleviate diverse pains. However, significant individual variations in analgesic effect of EA for both experiments and clinics were reported. According to the sensitivity of the analgesic response to EA stimulation, the subjects could be categorized into high responders (HR) and non responders (NR). However, the molecular mechanism of individual variability in the analgesic response to acupuncture stimulation is still uncertain. This study aims to investigate the potential gene expression in arcuate nucleus induced by 2Hz/100Hz electroacupuncture in HR and NR rats. Rats were given 2Hz or 100Hz electroacupuncture for 30 min and using cDNA microarrays to compare different gene expression in arcuate nucleus.

overall_design: Rats were exposed to different frequencies (2Hz or 100Hz) electroacupuncture stimulation for 30 min and nociceptive testing and returned to home cages for 1 hour before sacrificed. According to the sensitivity of the analgesic response to 2Hz or 100Hz EA stimulation, the rats divided into four groups: 2Hz-HR group, 2Hz-NR group, 100Hz-HR group and 100Hz-NR group. Subsequently analyzed their dorsal horn transcript profile using cDNA microarrays, the rats were without receiving electroacupuncture as control. The tissue of arcuate nucleus (Arc) of three rats was selected for transcript analysis in each group. The three control rats were mixed and labeled with cy5, each rat of experiment groups was labeled with cy3.

first: Ke

last: Wang

first: Fei

last: He

first: Libo

last: Lin

first: Qinghua

last: Zhang


title: A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (HumanOmni1-Quad)

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

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

summary: Systematic evaluation of eleven array platforms commonly used for CNV detection to address parameters of quality and CNV calling.

overall_design: 36 Samples

first: Dalila

last: Pinto

first: Jeffrey

middle: R

last: MacDonald


title: Comparison of gene expression profile of gilthead seabream mineralization-induced VSa13 cells against controls

status: Public on Jun 01 2011

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

institute: University of Padova

summary: In the present study, the Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) was used to compare expression profiles of mineralization-induced VSa13 cell cultures against untreated ones. ECM mineralization was induced for 4 weeks by supplementing medium with 50 µg/ml of L-ascorbic acid, 10 mM β glycerophosphate and 4 mM CaCl2. For each group, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of cells. Data analysis demonstrated that expression profiles were strongly affected by ECM mineralization with hundreds of genes differentially expressed with relevant fold-change.

overall_design: In this study, we analyzed six (6) cell samples, three (3) collected from untreated VSa13 cell cultures and three (3) collected from mineralization-induced VSa13 cell cultures. Gene expression profiling was performed using Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) (6 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal that was left after all the FE processing steps was ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Daniel

last: Tiago

first: Vincent

last: Laizé

first: Leonor

last: Cancela

first: Luca

last: Bargelloni


title: Comparison of gene expression profile of gilthead seabream mineralization-induced VSa16 cells against controls

summary: In the present study, the Agilent-016251 Sparus aurata oligo microarray platform (GEO accession: GPL6467) was used to compare expression profiles of mineralization-induced VSa16 cell cultures against untreated ones. ECM mineralization was induced for 4 weeks by supplementing medium with 50 µg/ml of L-ascorbic acid, 10 mM β glycerophosphate and 4 mM CaCl2. For each group, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of cells. Data analysis demonstrated that expression profiles were strongly affected by ECM mineralization with hundreds of genes differentially expressed with relevant fold-change.

overall_design: In this study, we analyzed six (6) cell samples, three (3) collected from untreated VSa16 cell cultures and three (3) collected from mineralization-induced VSa16 cell cultures. Gene expression profiling was performed using Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) (6 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal that was left after all the FE processing steps was ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.


title: Bj110 DMSO vs. Pterocarpan 6 (P6)

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

institute: University of Texas at Arlington

summary: Genome-wide transcriptional profiling of Bj110 cells treated with P6 (20 uM for 24 h).

overall_design: Three independent biological materials were prepared for cells treated with P6 or DMSO (vehicle control). A total 6 arrays which includes dye swap were analyzed.

first: Hae-In

last: Lee

first: Jin-Hwan

first: Ki-Hun

last: Park

first: Dipen

last: Sangurdekar


title: Suppression of TLR9-dependent gene expression in vivo mediated by TTAGGG motifs

city: Frederick

first: Dennis

last: Klinman

state: MD

department: CIP

institute: NCI Frederick

summary: Immunostimulatory CpG ODN trigger an innate immune response characterized by the rapid production of pro-inflammatory cytokines and chemokines, an effect that persists for days to weeks in vivo. Previous studies established that gene up-regulation is maximal 3 hr after CpG ODN treatment of normal mice {Klaschik et al. JLB 2009}. The immunostimulatory activity of CpG ODN is blocked by the addition of immunosuppressive ODN expressing multiple TTAGGG motifs. To clarify the mechanism underlying this suppression, changes in gene expresssion were evaluated by microarray in mice treated with 400 ìg of CpG ODN + 400 ìg of suppressive ODN.

overall_design: Data from 4 independent biological replicates/time point and treatment group and 6 untreated controls were used for all statistical analyses. A reference design was used. Reference cDNA vs. sample cDNA were hybridized to same array.


title: SCGB3A2 suppresses bleomycin-induced pulmonary fibrosis through activation of STAT1 and up-regulation of SMAD7

status: Public on Apr 30 2011

city: Yokohama

first: Reiko

last: Kurotani

state: Kanagawa

country: Japan

institute: Yokohama City University School of Medicine

summary: We report for the first time that secretoglobin (SCGB) 3A2, a novel cytokine-like molecule, predominantly expressed in pulmonary airways epithelium, drastically reduced the severity of lung fibrosis using bleomycin-induced mouse model.

overall_design: DNA microarrays were performed using RNAs isolated from mouse lungs in two experiments.  In the first experiments, mice were adminitered intravenously SCGB3A2 or PBS once daily for a week, starting on day 14 after BLM administration, and in the second experiments, SCGB3A2 or PBS was administered intravenously for 12 hrs.

first: Shioko

last: Kimura


title: Quantitative analysis of miRNA changes in CD4+ T cells responding to myelin antigen

status: Public on Apr 22 2011

city: Lodz

first: Marcin

middle: P

last: Mycko

address: Kopcinskiego 22

department: Department of Neurology

country: Poland

institute: Medical University of Lodz

summary:
Mice were immunized with either MOG35-55 in CFA or with CFA alone and 14 days later PLN cells were isolated and stimulated in vitro with MOG35-55 for 3 days followed by CD4+ T cell sorting.
Microarray analysis of miRNA expression profiles was performed comparing sorted CD4+ T cells from MOG35-55 in CFA immunized mice to CD4+ T cells from mice immunized with CFA alone.

overall_design: The data are from magnetic beads sorted CD4+ T cells from peripheral lymph nodes from 5 pooled animals per data point


title: Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA (ChIP)

status: Public on Apr 12 2011

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Genome binding/occupancy profiling by genome tiling array

summary: Occupancy profiling of Mlo3 in wild type and clr4∆ fission yeast Schizosaccharomyces pombe

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  Mlo3-Flag from asynchronous culture of fission yeast.

first: Ke

last: Zhang

first: Tamas

last: Fischer

first: Rebecca

middle: L

last: Porter

first: Jothy

last: Dhakshnamoorthy

first: Martin

last: Zofall

first: Ming

last: Zhou

first: Timothy

last: Veenstra

middle: I


title: Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA (expression)

type: Expression profiling by genome tiling array

summary:
Expression profile of Schizosaccharomyces pombe genome  in ∆mlo3, mlo3-A, mlo3-A∆h2a.z,  ∆cid14∆h2a.z and mlo3-A∆cid14 cells.
Expression profile of mutant cells compared to wild-type cells.

overall_design: Agilent 60mer oligonucleotide custom array containing probes spanning large portion of chromosome 2 at 50bp resolution was used to profile expression levels in mutant cells and to compare them to levels in wild-type cells.


title: Inflammatory gene expression in response to Francisella tularensis exposure in Balb/c mice

status: Public on Mar 01 2011

city: Salisbury

first: Jonathan

last: David

address: Porton Down

country: United Kingdom

institute: Dstl

summary: Francisella tularensis may enter the body thorugh the lungs and cause fatal infection. In this study the inflammatory response to the virulent strain of Francisella (Schu4) was mapped over a 96h time-course using a custom microarray.

overall_design: Six groups of 4 mice were exposed to aerosolised Francisella tularensis and a three groups exposed to vehicle only control (media only). Following exposure mice were culled at 4 timepoints (1, 24, 48 and 96h). RNA was extracted and run on the custom array.

first: Roman

last: Lukaszewski

first: Gareth

last: Griffiths


title: Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ES and iPS Cells during Reprogramming and Time in Culture

status: Public on Feb 15 2011

city: SAN DIEGO

first: GULSAH

last: ALTUN

state: CA

address: 3030 Science Park Rd. 3rd floor, room 3020

institute: THE SCRIPPS RESEARCH INSTITUTE

summary: Human embryonic and induced pluripotent stem cells (hESCs and iPSCs) are being considered as sources of differentiated cells for drug development and cell therapy. Genomic stability of these cells is important for in vitro studies, and is critical for clinical applications.  Of particular concern for cell therapy is the known association between genetic aberrations and tumorigenicity.  Our results highlight the dynamic nature of genomic abnormalities in pluripotent stem cell culture and the need for frequent genomic monitoring of pluripotent stem cells destined for transplantation in order to determine the impact of specific genomic changes on phenotypic stability and clinical safety.

overall_design: To map genomic abnormalities in pluripotent cells, we compared 130 hESC, 56 iPSC, 55 somatic stem cell and primary cell, and 67 tissue samples using high resolution SNP (single nucleotide polymorphism) analysis.

first: Louise

middle: C

last: Laurent

first: Igor

last: Ulitsky

first: Ileana

last: Slavin

first: Ha

last: Tran

first: Andrew

last: Schork

first: Robert

last: Morey

first: Candace

last: Lynch

first: Julie

last: Harness

first: Sunray

last: Lee

first: Maria

last: Barrero

first: Marina

last: Martynova

first: Franz-Josef

last: Muller

first: Ruslan

last: Semechkin

first: Vasiliy

last: Galat

first: Joel

last: Gottesfeld

first: Juan

last: Belmonte

first: Chuck

last: Murry

first: Hans

last: Keirstead

first: Hyun-Sook

last: Park

first: Ulrich

last: Schmidt

last: Laslett

first: Caroline

last: Nievergelt

first: Ron

last: Shamir

first: Jeanne

middle: F

last: Loring


title: Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (expression)

status: Public on Jan 07 2011

first: Shiv

last: Grewal

summary:
Expression profile of Schizosaccharomyces pombe genome  in asf1-1 and ∆hip1 cells.
Expression profile of mutant cells compared to wild-type cells.

first: Kenichi

last: Yamane

first: Takeshi

last: Mizuguchi

first: Bowen

last: Cui

first: Martin

last: Zofall

first: Ken-ichi

last: Noma


title: Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (ChIP-chip)

summary: Occupancy profiling of H3K9ac in fission yeast Schizosaccharomyces pombe

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of H3k9ac from asynchronous culture of fission yeast.


title: oct07-DNA methylation and small RNAs

status: Public on Apr 01 2011

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

summary: rs09-10_fwa - oct07. Impact of loss of DNA methylation and small interference RNAs (siRNAs) on gene expression. Mutants impaired for the DNA methylation maintenance pathway and for the RNA interference machinery were compared to mutants simultaneously impaired for both machineries to estimate their impact on genome activity.

overall_design: 8 dye-swaps. Gene knockout.

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Vincent

last: Colot

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice

status: Public on Dec 25 2010

city: Blacksburg

first: Andy

last: Pereira

state: VA

address: Washington Street MC0477

department: Virginia Bioinformatics Institute

institute: Virginia Tech

summary:
Cellulose from plant biomass is the largest renewable energy resource of carbon fixed from the atmosphere, which can be converted into fermentable sugars for production into ethanol.
However, the cellulose present as lignocellulosic biomass is embedded in a hemicellulose and lignin matrix from which it needs to be extracted for efficient processing.
Here, we show that expression of an Arabidopsis transcription factor SHINE (SHN) in rice, a model for the grasses, causes a 34% increase in cellulose and a 45% reduction in lignin content.

overall_design: Rice genotypes expressing the Arabidopsis SHN2 gene hereafter called rice AtSHN lines were used in this study. Progenies of three independent AtSHN lines were grown in controlled growth chambers. For all analyses, six plants were used for each of the two transgenic lines and WT. For total RNA isolation, rice leaf tissue of WT and AtSHN lines was used. Samples were hybridized to the rice Affymetrix GeneChip.

first: Madana

last: Ambavaram

first: Arjun

last: Krishnan

first: Kurniawan

last: Trijatmiko


title: Comparison of constitutional and replication stress-induced genome structural variation by SNP array and mate-pair sequencing

status: Public on Dec 18 2010

city: Ann Arbor

first: Thomas

middle: E.

last: Wilson

address: 2065 BSRB, 109 Zina Pitcher

department: Department of Pathology

institute: University of Michigan

summary: Copy number variants (CNVs) are a major source of genetic variation in human health and disease.  Previous studies have suggested replication stress, such as that caused by the polymerase inhibitor aphidicolin, as a causative factor in CNV formation, but existing data are technically limited in the quality of the comparisons which can be made to experimentally induced variants.  Here we used 1M feature single-nucleotide polymorphism (SNP) arrays and mate-pair sequencing as high resolution methods for characterizing CNVs in a common set of samples, to compare both the properties of constitutional and induced CNVs as well as the utility of the two methods in an experimental setting.  Although the optimized methods provided complementary information, sequencing was more sensitive to small variants and provided superior structural descriptions that allowed some CNVs to be associated with inversions, ectopic duplications or LINE insertions.  The majority of constitutional and all aphidicolin-induced CNVs appear to be formed via homology-independent mechanisms, while aphidicolin-induced CNVs were of a larger median size than constitutional events even when mate-pair data were considered.  Aphidicolin thus appears to stimulate formation of CNVs that closely resemble human pathogenic CNVs and the subset of larger nonhomologous constitutional CNVs.

overall_design: One untreated and one aphidicolin-treated subclone of human fibroblast cell line HGMDFN090 were analyzed by Illumina HumanOmni1-Quad SNP array and low-density mate-pair sequencing.

last: Arlt

first: Alev

last: Ozdemir

first: Shanda

last: Birkeland

first: Robert

middle: H

last: Lyons

last: Glover

middle: E


title: OsNPR1-dependent rice genes

status: Public on Dec 24 2010

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

institute: National Institute of Agrobiological Sciences

summary: NPR1 is a central positive regulator of salicylic-acid (SA)-mediated defense signaling in Arabidopsis. Here, we report characterization of OsNPR1, an Oryzae sativa (rice) ortholog of NPR1, focusing on its role in blast disease resistance and identification of OsNPR1-regulated genes followed by their comparison with NPR1-regulated genes in Arabidopsis. Blast resistance tests using OsNPR1–knockdown and –overexpressing rice lines indicated that OsNPR1 plays an essential role in benzothiadiazole-induced blast resistance. Genome-wide transcript profiling using OsNPR1–knockdown lines revealed that 358 genes out of 1,228 BTH-upregulated genes and 724 genes out of 1,069 BTH-downregulated genes were OsNPR1 dependent with respect to their BTH responsiveness, indicating that OsNPR1 plays a major role in the downregulation. Inspection of OsNPR1-dependent genes revealed that many genes involved in photosynthesis and chloroplastic translation and transcription were downregulated by BTH in an OsNPR1 dependent manner, indicating that photosynthesis and chloroplast activities is coordinately suppressed by OsNPR1 in response to BTH-induced activation of SA-signaling pathway. ABA-responsive genes were also OsNPR1-dependently downregulated, suggesting antagonistic interaction of SA signaling on ABA signaling. None of 11 BTH-upregulated genes for WRKY transcription factors was OsNPR1 dependent, whereas most of those are NPR1-dependently upregulated in Arabidopsis, indicating that the role of OsNPR1 is distinct from that of NPR1 in Arabidopsis. We discuss the significance of OsNPR1-regulated gene expression in SA-regulated defense program and the role of OsNPR1 in rice SA-signaling pathway that is branched to OsNPR1- and rice WRKY45-dependent sub-pathways.

overall_design: mock-treated wild-type (Nipponbare) rice, benzothiadiazole (BTH)-treated wild-type rice, mock-treated WRKY45-knockdown rice (2 lines) and BTH-treated WRKY45-knockdown rice (2 lines) were analyzed in four biological replicates.

first: Shoji

last: Sugano


title: Aspergillus niger WT: Control vs. steam-exploded sugarcane induction

status: Public on Oct 20 2010

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

institute: University of Sao Paulo

summary: Transcriptional profiling of A. niger comparing WT strain vs. ΔXlnR strain treated with steam-exploded sugarcane bagasse (SESB) for 6, 12 and 24 h. The main objective was to identifiy genes related to cellulases and hemicellulases, comparing the differences between WT strain and the strain with the disrupted xylanolytic transcriptional activator gene, XlnR, after treatment with steam-exploded sugarcane. The experiment was further validated by real-time PCR, mass spectrometry of secreted proteins and enzymatic assays.

overall_design: Three-condition experiment : WT-SESB or ΔXlnR-SESB for 6, 12 and 24 h at 30 oC in batch culture. Firstly, WT and ΔXlnR strains were grown in minimal medium with fructose as carbon source (control), and then transferred to SESB as carbon source.


title: Expression analysis of Streptococcus pyogenes NZ131 serR-

status: Public on Nov 15 2010

city: Chicago

first: Michael

last: Federle

state: IL

address: 900 S Ashland Ave. MC870

department: Microbiology & Imm. / Cntr Pharm Biotech

institute: University of Illinois at Chicago

summary:
Whole genone expression profile comparing wild-type NZ131 to serR deletion mutant, grown in C-medium
Mutants and interpretation are described further in the manuscript to be submitted: LaSarre and Federle, 2010. Title: Regulation and Consequence of Serine Catabolism in Streptococcus pyogenes.

overall_design: A two chip study using total RNA recovered from three separate wild-type cultures of Streptococcus pyogenes NZ131 and three separate mutant cultures of Streptococcus pyogenes NZ131 seR-, pooled following RNA extraction

first: Breah

last: LaSarre


title: Let-7 microRNAs are developmentally regulated in circulating human erythroid cells

status: Public on Jun 21 2010

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: MicroRNA are ~22nt-long small non-coding RNA that negatively regulate protein expression through mRNA degradation or translational repression in eukaryotic cells. Based upon their importance in regulating development and terminal differentiation in model systems, erythrocyte microRNA profiles were examined at birth and in adults to determine if changes in their abundance coincide with the developmental phenomenon of hemoglobin switching. Expression profiling of microRNA was performed using total RNA from 4 adult peripheral blood samples compared to 4 cord blood samples after depletion of plasma, platelets, and nucleated cells. Labeled RNA was hybridized to custom spotted array containing 474 human microRNA species (miRBase release 9.1). Total RNA from Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines provided a hybridization reference for all samples to generate microRNA abundance profile for each sample. Among 206 detected miRNA, 79% of the miRNA were present at equivalent levels in both cord and adult cells. By comparison, 40 microRNA were up-regulated and 4 microRNA were down-regulated in adult erythroid cells (fold change > 2; p < 0.01). Among the up-regulated subset, the let-7 miRNA family consistently demonstrated increased abundance in the adult samples by array-based analyses that were confirmed by quantitative PCR (4.5 to 18.4 fold increases in 6 of 8 let-7 miRNA). Profiling studies of mRNA in these cells additionally demonstrated down-regulation of ten let-7 target genes in the adult cells. These data suggest that a consistent pattern of up-regulation among let-7 miRNA in circulating erythroid cells occurs in association with hemoglobin switching during the fetal-to-adult developmental transition in humans.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: Expression profiling of microRNA was performed using biological replicates from 4 adult peripheral blood samples compared to 4 cord blood samples after depletion of plasma, platelets, and nucleated cells. Total RNA from Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines provided a hybridization reference for all samples.


title: Gene amplification of the transcription factor DP1 and the CTNND1 in human lung cancer

status: Public on Apr 11 2010

city: L´Hospitalet de Llobregat

first: Sandra

last: Castillo

address: Avda. Gran Via 199-203

country: Spain

institute: IDIBELL-PEBC

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

summary: The search for novel oncogenes is important because these could be the target of future specific anticancer therapies. In the present work, we report the identification of novel amplified genes in lung cancer. In order to find out novel amplified genes in lung cancer, we aligned the gene expression data of 69 human lung tumors according to the position of transcripts in the human genome and searched for clusters of overexpressed genes. We found a cluster in chromosomes 13q34 and 11q12 with gene overexpression in four of these tumors. Then, we performed FISH analysis in these amplicons, which clearly evidenced the presence of high level copy number in these chromosomal regions. We performed SNP arrays-based in the tumors that carried gene amplification. The results clearly evidenced the presence of a high level copy number amplicon in these specimens.

overall_design: We determined the genomic copy number profile of four squamous cell carcinoma (SCC) tumours using a SNP array, the Illumina Infinium HumanOmni1-Quad BeadChip.

first: Maria

last: Alonso

first: Guillermo

last: Pita

first: Javier

last: Benítez

first: Montse

last: Sanchez-Cespedes


title: Shigella Apoptosis Arrays

status: Public on Jun 12 2010

first: Douglas Scott

last: Merrell

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

summary: Array data from HeLa cells that remained Uninfected or were infected with wildtype S. flexneri serotype 2a strain 2457T.  These groupings are further divided such that Uninfected or Infected cells remained untreated or were treated with the apopotosis inducer staurosporine (STS).  The design of the experiment was a time course and samples were harvested at the indicated time points (hr).  All hybridizations were conducted against a common reference sample.

first: Douglas

middle: S


title: Cytb1-1-Ascorbate metabolism in plants: physiological function and biochemical properties of cytochrome b561

status: Public on Apr 01 2010

first: Soubigou-Taconnat

last: Ludivine

institute: INRA

summary:
What is the physiological function of cytochrome b561 in Arabidopsis thaliana - We want to check which possible changes occur in gene expression by knocking out the AtCytb1 gene.

au08-01_cytb561 - cytb1-1

Keywords: gene knock out

overall_design: 4 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Kim

last: Van beek

first: Marie-Laure

last: Martin-Magniette


title: Impact of c-MET Signaling on Liver Regeneration

status: Public on Aug 01 2010

first: Snorri

last: Thorgeirsson

address: 37 Convent Dr. # 4146

department: Laboratory of Experimental Carcinogenesis

institute: National Cancer institute/NIH

summary: c-Met is a receptor tyrosine kinase for hepatocyte growth factor (HGF). Previous work has established that HGF plays a pivotal role in regulating the onset of S phase and DNA replication following partial hepatectomy. In this study, we used c-Met conditional knockout mice (MetLivKO) in which c-met gene is inactivated in postnatal hepatocytes by Alb-Cre recombinase to directly address the net biological outcome of c-Met on liver regeneration. The priming events appear to be intact in MetLivKO livers. Up-regulation of stress response (e.g MAFK, IKBZ, SOCS3) and early growth response (e.g. MYC, DUSP1 and 6) genes as judged by microarray profiling was similar in c-Met deficient regenerating livers as compared to Alb-Cre controls. This was consistent with an early induction of NF-kB, STAT3, and MAPK/ERK. Nevertheless, in the absence of c-Met signaling in the hepatocytes, ERK phosporylation rapidly declined although it remained high in Cre-Ctrl livers, and MetLivKO mice displayed impaired liver regeneration as determined by a decrease in BrdU incorporation and a delay in timely progression into mitosis. Upstream signaling pathways involved in the blockage of G2-M transition included lack of EGR1 transcription factor induction, and inability to up-regulate the levels of cdc2, aurora B and Mad2 followed by defective histone 3 phosphorylation and lag in chromatin condensation. However, after a delayed passage through G2 phase, c-Met deficient cells eventually entered mitosis. In culture, EGF treatment increased proliferation of MetLivKO hepatocytes and restored expression levels of cell cycle regulators aurora B and Mad2 albeit to a lesser degree as compared to Cre-Ctrl hepatocytes. In conclusion, our results assign a novel function for HGF/c-Met signaling in regulation of G2/M transition during liver regeneration and implicate EGR1 as a potential G2/M target of HGF/c-Met pathway.

overall_design: Multiple repeats were done of eight timepoint conditions (0, 0.5, 2, 12, 24, 36, 42, and 48 hours) using wild type and knock-out mice. All samples were reverse-fluor labelled. A pooled sample of wild type liver was used as reference.


title: Peripheral blood stem cell gene profiling

summary:
Mobilized-peripheral blood hematopoietic stem cells (HSCs) have been used for transplantation, immunotherapy, and cardiovascular regenerative medicine. Agents used for HPC mobilization include G-CSF and the CXCR4 inhibitor AMD3100. The HSCs cells mobilized by each agent may contain different subtypes and have different functions. To characterize mobilized HSCs used for clinical applications, microRNA (miRNA) profiling and gene expression profiling were used to compare AMD3100-mobilized CD133+ cells from 4 subjects, AMD3100 plus G-CSF-mobilized CD133+ cells from 4 subjects and G-CSF-mobilized CD34+ cells from 5 subjects. The HSCs were compared to peripheral blood leukocytes (PBLs) from 7 subjects.
Keywords: cell type comparison design


title: Peripheral blood stem cell microRNA profiling

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
human gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus macacae

overall_design: microRNA (miRNA) profiling were used to compare AMD3100-mobilized CD133+ cells from 4 subjects, AMD3100 plus G-CSF-mobilized CD133+ cells from 4 subjects and G-CSF-mobilized CD34+ cells from 5 subjects. The HSCs were compared to peripheral blood leukocytes (PBLs) from 7 subjects.


title: SelT knockdown mouse fibroblast cells vs control cells

status: Public on Nov 01 2009

first: Dolph

last: Hatfield

address: 37 Convent Drive, Rm. 6032A

department: LCP

institute: NIH/NCI

summary: Analysis of gene expression in NIH 3T3 cells stably knockdown for Selt (GenBank accession number NM_001040396) using vector based siRNA technique in comparison to gene expression of vector transfected NIH 3T3 cells.

overall_design: siSelT-1 construct (spanning nucleotides 205-224 of Selt, GenBank accession number NM_001040396) vs vector control; siSelT-5 construct (spanning nucleotides 971-989 of Selt, GenBank accession number NM_001040396) vs vector control; Two replicates per array for each oligos were carried out at different time points using RNA from different cultures of knockdown cells.

first: Aniruddha

last: Sengupta

first: Bradley

middle: A

last: Carlson

first: Vyacheslav

middle: M

last: Labunskyy

first: Vadim

middle: N

last: Gladyshev


title: MicroRNA expression differentiates histology and predicts survival of lung cancer

status: Public on Mar 11 2010

first: Francesco

last: Marincola

summary: Abstract. Background. Treatment for lung adenocarcinoma (AD) and squamous cell carcinoma (SQ) is similar and shows comparable poor efficacy. We investigated whether microRNA (miR) expression profiles can differentiate histological subtypes, predict survival, and suggest histology-specific targets for treatment. Methods. We analyzed miR expression in 165 AD and 125 SQ tissue samples from the Environmental And Genetics in Lung cancer Etiology (EAGLE) study using a custom oligo array with 440 human mature antisense miRs. We compared miR expression profiles using t-tests and F-tests and accounted for multiple testing using global permutation tests. We categorized miR-targeted genes using Gene Ontology. We assessed the association of miR expression with clinical outcome using log-rank tests, Cox proportional hazards and survival risk prediction models, accounting for demographic and tumor characteristics. Findings. MiR expression profiles strongly differed between AD and SQ (global p<0.0001), particularly in the early stages. All members of the let-7 family and other oncosuppressor miRs were down-regulated in SQ, while oncomiRs like miR-21 were up-regulated in AD. The miRs with the strongest expression differences are located on chromosome loci most often altered in lung cancer (e.g., 3p21-22). Major findings were confirmed by QRT-PCR in EAGLE samples and in an independent cohort. In SQ, low expression of miRs down-regulated in the histology comparison was associated with 1.2 to 3.6-fold increased mortality risk. A 5-miR signature significantly predicted survival for SQ. Interpretation. We identified a miR expression profile that strongly differentiated AD from SQ and had prognostic implications. These findings may lead to histology-based therapeutic approaches.

overall_design: We conducted a large miR expression study in 290 subjects, including 165 AD and 125 SQ patients, within the Environment And Genetics in Lung cancer Etiology (EAGLE) study. The reference sample is derived from an EBV cell line.


title: Short and long-term changes in gene expression mediated by the activation of TLR9

status: Public on Jan 08 2010

first: Dennis

last: Klinman

institute: NCI Frederick

summary: CpG DNA binds to Toll-like receptor 9 to stimulate a strong innate immune response. Despite extensive studies of TLR9 mediated signal transduction, the scope of CpG-induced changes in gene expression is incompletely understood. In particular, the prolonged effects of CpG ODN (oligodeoxynucleotide) on gene activation have not been investigated despite evidence that a single dose of CpG ODN alters immune reactivity for several weeks. This study used gene expression analysis to monitor changes in mRNA levels for 14 days, and identified the genes, pathways, functional groups and regulatory networks triggered in vivo following CpG ODN administration. Two discrete peaks of gene activation (at 3 hr and 5 days) were observed after CpG administration. Both the regulation and function of genes activated during the second peak differed from those triggered shortly after CpG administration. Initial gene up-regulation corresponded to a period when TLR9 ligation stimulated genes functionally associated with the generation of innate and adaptive immune responses (e.g. the NF-kB and B-cell receptor pathways). The second peak reflected processes associated with cell division (e.g., cell cycle and DNA replication & repair). Whereas TNF and IFNG played central roles regulating the first peak of activation, E2F1, E2F2, BRCA1, and HRAS had major impact on the networks controlling the second peak. The complex bimodal pattern of gene expression elicited by CpG ODN administration provides novel insights into the long term effects of CpG DNA on genes associated with immunity and cell proliferation.

overall_design: Data from 4 independent biological replicates/time point (9 time points) and 6 untreated controls were used for all statistical analyses. A reference design was used. Reference cDNA vs. sample cDNA were hybridized to same array.


title: The effect of PPARa siRNA on endothelial cells treated with fenofibrate

status: Public on Aug 24 2009

city: Cambridge

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

institute: University of Cambridge

summary: Fenofibrate is a synthetic ligand for the nuclear receptor peroxisome proliferator-activated receptor (PPAR) alpha, but there are reports that fenofibrate affects endothelial cells in PPARa-independent manner. In order to identify PPARa-dependently and PPARa-independently regulated transcripts we generated microarray data from human endothelial cells treated with fenofibrate with and without siRNA-mediated knock-down of PPARa.

overall_design: In this study, we generated microarray data from human umbilical vein endothelial cells (HUVECs) treated with fenofibrate with pretreatment PPARa or control siRNA. There are four time points (4, 8, 12 and 18hours) (n=1 at each time point).

first: Hiromitsu

last: Araki

first: Yoshinori

last: Tamada

first: Seiya

last: Imoto

first: Ben

last: Dunmore

first: Deborah

last: Sanders

first: Sally

last: Humphrey

first: Masao

last: Nagasaki

first: Atsushi

last: Doi

first: Yukiko

last: Nakanishi

first: Kaori

last: Yasuda

first: Yuki

last: Tomiyasu

first: Kousuke

last: Tashiro

first: Cristin

last: Print

first: D

first: Satoru

last: Kuhara

last: Miyano


title: Phosphate depletion: A novel trigger for Mycobacterium tuberculosis persistence

status: Public on Sep 22 2009

city: Baltimore

first: Petros

last: Karakousis

address: 1550 Orleans street

department: Medicine

institute: John Hopkins University school of medicine

summary: These data represent the global gene expression profile of Mycobacterium tuberculosis after 24 hrs and 72 hrs of inorganic phosphate starvation. Differentially regulated genes appear to include those encoding proteins involved in adaptation to phosphate starvation, namely those involved in phosphate regulation and phosphate assimilation, as well as those involved in the stringent response.

overall_design: To investigate genes involved in phosphate regulation and assimilation, as well as the stringent response, three biological replicates were prepared from log phase cultures in phosphate-replete medium (25mM phosphate),which served as control, and 24 and 72 hrs of phosphate-starved cultures served as sample replicates.  After purification of total RNA from above cultures, fluorescent labeled cDNAs were generated and used for dual channel hybridization to perform genome-wide  microarray studies. Three slides were used for each time point. Collected microarray data were normalized by global and local normalization. Genes with ≥ 2-fold change in expression in all three hybridizations and q-value ≤0.01 were defined as being significantly differentially regulated. our data showed  that genes related to phosphate regulation and assimilation as well as the stringent response were dramatically upregulated.

first: Dalin

last: Rifat


title: The effect of fenofibrate on endothelial cells

first: D. Stephen

last: Charnock-Jones

overall_design: In this study, we generated microarray data from human umbilical vein endothelial cells (HUVECs) treated with fenofibrate. Time 0 indicates the start point of observation immediately prior to exposure to the 25umol fenofibrate. There are five time points (2, 4, 6, 8, and 18hours) (n=3 at each time point). The control is untreatment HUVEC (n=4).

first: Hiromitsu

last: Araki


title: Illumina HapMap YRI (HumanOmni1-Quad v1)

status: Public on Jul 27 2009

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

summary: HapMap samples

overall_design: 90 samples from HumanOmni1-Quad_v1_90YOR_FinalReport.csv


title: Illumina HapMap CEU (HumanOmni1-Quad v1)

summary: HapMap samples

overall_design: 88 samples from HumanOmni1-Quad_v1_88CEU_FinalReport.csv


title: Illumina HapMap CHB and JPT (HumanOmni1-Quad v1)

summary: HapMap samples

overall_design: 89 samples from HumanOmni1-Quad_v1_89CHB-JPT_FinalReport


status: Public on Dec 16 2009

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary:
Full title: Eccentric exercise activates novel transcriptional regulation of hypertrophic signaling pathways not affected by hormone changes.
Unaccustomed eccentric exercise damages muscle tissue stimulating mechanisms of recovery and remodeling that may be affected by cellular protection by the sex hormone 17β-estradiol (E2). Using cDNA microarrays, we screened for differences in mRNA expression caused by E2 and eccentric exercise. After randomly assignment to 8 days of either placebo (CON) or E2 (EXP), eighteen men performed 150 single-leg eccentric contractions.  Muscle biopsies were collected at baseline (BL), following supplementation (PS), +3 hours (3H) and +48 hours (48H) after exercise. Serum E2 concentrations increased significantly with supplementation (P < 0.001) but did not affect microarray results. Exercise led to early transcriptional changes in striated muscle activator of Rho signaling (STARS), Rho family GTPase 3 (RND3), mitogen activated protein kinase (MAPK) regulation and the downstream transcription factor FOS. Targeted RT-PCR analysis identified concurrent induction of negative regulators of calcineurin signaling RCAN (P < 0.001) and HMOX1 (P = 0.009). Protein contents were elevated for RND3 at 3H (P = 0.02) and FOS at 48H (P < 0.05). These findings indicate that early RhoA and NFAT signaling and regulation are altered following exercise for muscle remodeling and repair, but are not affected by E2.

overall_design: Eighteen young healthy men volunteered as participants in this study. All subjects were pre-screened to ensure that they were healthy, fit and had not regularly participated in resistance exercise in the preceding 6 months. Body composition was measured using dual energy x-ray absorptiometry (DEXA) scans (Hologic QDR 1000W, Waltham, MA). Thigh muscle cross-sectional area was calculated using anthropomorphic measurements of mid-thigh circumference and skinfold thickness. The subject demographics were (mean ± SD): age, 21 ± 2 y; height, 181 ± 5 cm; weight, 76.9 ± 12.8 kg. Subjects were assigned in a randomized, double-blind manner to either a control (CON, N=9) or experimental (EXP, N=9) group. CON subjects consumed 400 mg glucose polymer (Polycose; Abbott Laboratories, Ross Division, St. Laurent, Quebec, Canada) for 10 days. EXP subjects consumed ~300 mg glucose with 1 mg E2 (Estrace; Shire BioChem, Inc., St. Laurent, Quebec, Canada) for 2 days followed by 2 mg E2 for 8 days. On the morning of the ninth day, subjects reported to the laboratory and performed the exercise protocol. Supplementation continued until the day of the final biopsy and blood collection to maintain serum E2 concentrations throughout the collection protocol. Subjects in both groups were instructed to take one pill at the same time each day and return any unused pills.  On the testing day, following a short warm-up (10 min of light cycling), subjects were seated in a Biodex isokinetic dynamometer (System 3, Biodex Medical Systems Inc., Ronkonkoma, NY) with their right leg strapped to a lever arm. The lever arm was programmed to extend their leg to 150º of flexion (where 180º is full extension) at a moderate speed (30º/s), then flex their leg to 90°of flexion at a faster speed (120°/s). During the flexion phase, subjects were instructed to attempt to maximally resist flexion of the knee (i.e. voluntary ‘maximal’ contraction) against the descending lever arm throughout the entire range of motion. The complete test consisted of 15 sets of 10 repetitions, each set separated by 1 minute of rest. Prior to each tissue collection, subjects abstained from any other form of physical exertion (within 72 h), avoided alcohol (within 48 h), ate their habitual diet (within 48 h), and abstained from caffeine (within 12 h). Each subject consumed a 350 Kcal defined formula diet (57% carbohydrates, 15% protein and 28% fat) two hours before each muscle biopsy and did not eat again until after the final biopsy of each session was taken. Muscle biopsies were taken from the vastus lateralis of the control (left) leg during the familiarization session (baseline, BL) and after 8 days of supplementation (post supplementation, PS) and the exercised (right) leg 3 hours (3H) and 48 hours (48H) after exercise, in anatomically distinct sites approximately 6 cm apart. Blood was drawn from the antecubital vein at the same collection times. Muscle and blood samples were processed and stored for future measurements.

first: Lauren

middle: G

last: MacNeil

first: Alan

last: Hubbard

first: Steven

middle: K

last: Baker

first: Mark

last: Tarnopolsky


title: compare haiku mutants with wildtype-Study of small seed mutants.

status: Public on Jul 08 2009

first: Soubigou-Taconnat

last: Ludivine

department: URGV

summary:
au07-11_haiku - compare haiku mutants with wildtype - What are other genes involved in haiku pathway? - IKU1, IKU2 belong to same pathway which involved in seed development. Using array analysis try to find other components of this pathway.

Keywords: gene knock out

overall_design: 10 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Frederic

last: Berger

first: Marie-Laure

last: Martin-Magniette


title: Adaptation of Root Architecture to Abiotic Stress

status: Public on May 28 2009

city: Evry Cedex

first: Agnes

last: Yu

address: 2 rue Gaston Cremieux CP 5708

summary:
rs08-01_met2 - comparative analysis of catma  chips  with a met2 overexpression line - Role of the MET2 methyltransferase on methylation and gene expression in arabidopsis - Comparison of transcription in roots and aerial parts of one week-old plants from two lines (WT and MET2 overexpressor)

Keywords: organ comparison,wt vs mutant comparison

first: Martin

last: Crespi

first: Caroline

last: Hartmann


title: Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent human gut symbiont

status: Public on Jun 01 2009

first: Eric

middle: Charles

last: Martens

address: 1150 West Medical Center Drive

institute: University of Michigan Medical School

summary: Analysis of B. thetaiotaomicron trans-envelope signaling mutants in ECF-sigma factors, anti-sigma factors and SusC-like transporters.

platform_organism:
Bacteroides thetaiotaomicron
Bifidobacterium longum

overall_design: B. thetaiotaomicron mutants were transcriptionally profiled after growth in vitro in either minimal medium plus glucose or minimal medium plus neutral O-glycans

first: Jeffrey

last: Gordon


title: seed specific genes-Establishing the network of seed gene expression and analysis of its biodiversity

status: Public on May 30 2009

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

summary:
gnp3_tri33-arabidoseed - seed specific genes - WP3 : Biodiversity of seed traits : state of the art - This experiment aimed to identify the genes expressed in the seeds vs siliques (easiest to harvest), and to know if the expression pattern of the whole silique could provide a valuable information.

Keywords: organ comparison

overall_design: 3 dye-swap - CATMA arrays

first: Samira

last: Elftieh

first: Michel

last: Caboche

middle: P


title: preliminary experiment:repetability-Establishing the network of seed gene expression and analysis of its biodiversity

summary:
gnp3_tri33-arabidoseed - preliminary experiment:repetability - WP3 : Biodiversity of seed traits : state of the art - The third experiment is a comparison of the transcriptome of two parents (Bay0,Sha) and two RILs (104, 140) in loop experimental design. Plants are grown in individual pots on a tray.Flowers were tagged on the flowering day using colored tape. Siliques were harvested 10 days after flowering, freezed in liquid nitrogene and stored at -80degreeC until RNA extraction.

Keywords: genotype and ecotype comparison

overall_design: 8 dye-swap - CATMA arrays

middle: L


title: Gene expression of lpp2 KO mutant in response to ABA.

status: Public on Jul 01 2009

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

summary:
Transcriptomic study of lpp2 KO mutant in response to abcsisic acid - Fully developed rosette leaves were immersed for 1 min in a solution of 10-5 M ABA with 0.1% DMSO and 0.05%silwet. RNA are extracted after a 3h incubation. This treatment is compared to control (1 min immersion in 0.1% DMSO and 0.05%silwet) then 3h incubation.

Keywords: treated vs untreated comparison

overall_design: 4 dye-swap - CATMA arrays

first: Emmanuelle

last: Jeannette


title: seed development-Establishing the network of seed gene expression and analysis of its biodiversity

summary:
gnp3_tri33-arabidoseed - seed development - WP3 : Biodiversity of seed traits : state of the art - This experiment is a time course performed to choose the best harvesting point to maximise the number of detectable transcripts (8, 10, 12 and 14 dap).

Keywords: time course


title: Transcriptome analysis of fry2 mutants-Transcriptome analysis of fry2 mutants

status: Public on Apr 15 2009

summary:
ra08-01_cpl1 - transcriptome analysis of fry2 mutants - Compare the transcriptome of 2 mutants affected in FRY2 (fry2-1 and 14-5sep) to control plants. - The Arabidopsis 14-5sep mutant was isolated as overexpressing a NII::LUC construct fusing a tobacco nitrite reductase gene with the luciferase reporter gene. This mutant overexpressed also the endogenous Arabidopsis nitrite reductase gene. Map-based cloning showed that the 14-5 sep mutant was affected in the FRY2 gene. Transciptome analysis was performed on both the 14-5sep and the fry2-1 mutants and their respective controls (either the C24 ecotype containing the RD29A::LUC transgene for fry2-1 or the Col0 accession containing the NII::LUC transgene for the 14-5sep mutant) to analyze which genes are differentially expressed in the mutants versus control plants.
Keywords: gene knock out

first: Hoai-Nam

last: Truong


title: Comparison of simple mutants gcn5 and hd1 and double mutant gcn5 hd1.

status: Public on Apr 11 2009

address: 2 rue gaston crémieux

summary:
rs05-09_histone-acetylase - gcn5 - Different genes show an opposed expression profile in gcn5 compared to hd1. For these genes, the double mutant might show an expression similar to the wild type.  - gcn5, hd1 or double mutant gcn5hd1 were grown on MS during 10 days (1.03 boyes stage).

Keywords: gene knock out

overall_design: 3 dye-swaps - CATMA arrays

first: Dao-xiu

middle: X

last: Zhou

first: Olivier

last: Pichon


title: plp2 bc 1-Functional analysis of lipid acyl hydrolases in Arabidopsis antimicrobial defense

status: Public on May 05 2009

first: Soubigou-Taconnat

last: Ludivine

summary:
Effects of deregulation of a lipid acyl hydrolase gene (PLP2, At2g26560) on global transcriptome upon infection by Botrytis cinerea. This deregulation affects resistance levels against fungal and bacterial pathogens, likely by perturbing the biosynthesis of oxylipins. Oxylipins are fatty acid-derived compounds (example:jasmonic acid) with diverse signaling or antimicrobial properties. - 2500 spores of Botrytis cinerea were pipetted on 4 infection sites per adult leaf. Leaf material was harvested at 0, 24 and 48 hours. 3 plant genotypes were used (Col-0) : PLP2- silenced (RNAi), control, PLP2-overexpressors.

Keywords: normal vs rnai mutant comparison,time course,treated vs untreated comparison

overall_design: 5 dye-swap - CATMA arrays

first: Thierry

last: Heitz


title: af13_plp2 - plp2 paraquat - Functional analysis of lipid acyl hydrolases in Arabidopsis antimicrobial defense

summary:
Effects of deregulation of a lipid acyl hydrolase gene (PLP2, At2g26560) on global transcriptome upon infection by Botrytis cinerea. This deregulation affects resistance levels against fungal and bacterial pathogens, likely by perturbing the biosynthesis of oxylipins. Oxylipins are fatty acid-derived compounds (example:jasmonic acid) with diverse signaling or antimicrobial properties. - 10 uM Paraquat was infiltated in mesophyll of leaves with a syringe without needle. Leaf material was harvested at 0, 4 and 18 hours later. 3 plant genotypes were used (Col-0 ecotype) : - siPLP2 (RNAi-silenced) - pBIN (empty pBIN-transformed) - PLP2OE (PLP2-overexpressors).

Keywords: gene knock in (transgenic),time course

overall_design: 6 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou


title: plp2 botrytis cinerea 2-Functional analysis of lipid acyl hydrolases in Arabidopsis antimicrobial defense

summary:
Effects of deregulation of a lipid acyl hydrolase gene (PLP2, At2g26560) on global transcriptome upon infection by Botrytis cinerea. This deregulation affects resistance levels against fungal and bacterial pathogens, likely by perturbing the biosynthesis of oxylipins. Oxylipins are fatty acid-derived compounds (example:jasmonic acid) with diverse signaling or antimicrobial properties. - 5000 spores of Botrytis were pipetted on 4 infection sites per ault leaf. Leaf material was harvested at 0,1,2,3 days later. 3 plant genotypes were used (Col-0 ecotype): siPLP2 (RNAi-silenced),pBIN (empty pBIN-transformed),PLP2OE (PLP2-overexpressors).

Keywords: gene knock in (transgenic),normal vs rnai mutant comparaison,time course

first: Marie-Laure

last: Martin-Magniette


title: Individualized analysis of subcutaneous and omental abdominal adipose tissue from non-obese and obese subjects

status: Public on Apr 03 2009

city: Quebec

first: Katherine

last: Cianflone

state: Quebec

address: 2725 Ste Foy

institute: Laval University

summary: Individualized analysis through expression profiling of 20,000 probes in 28 tissue samples evaluated in subcutaneous and omental adipose tissue obtained during surgical intervention in non-obese and obese patients. Patients consisted of men and women of varying body size (lean to severely obese). Samples were collected at the time of operation in the fasting state.

overall_design: Samples consisted of subcutaneous and omental adipose tissue as well as a blood sample from lean and obese men and women removed in the fasting state at the time of surgery.

first: Robin

last: MacLaren


title: Drosophila melanogaster transcriptional profiling over life span: Indy vs. Controls

status: Public on Mar 08 2009

city: Providence

first: Nicola

last: Neretti

state: RI

address: Box G-L158

institute: Brown University

summary:
Transcriptional profiling of Indy long lived flies and controls over the course of their entire lifespan.

Mutations in the Indy gene extend life span in Drosophila melanogaster. This study investigates the changes in gene expression over time in Indy206 flies heterozygous over Canton-S (Indy206/CS) and compares them to genetically matched heterozygous controls (2216/CS). Samples from both fly strains were collected at age: 5, 10, 20, 30, 40, 50, 70 and 80.

overall_design: mRNA samples were collected from the head and thorax of Indy206 and genetically matched control male adult flies at day 5, and every 10 days from day 10 to day 80 (day 60 excluded) and hybridized to two-color microarrays

first: Blanka

last: Rogina

first: Stephen

last: Helfand


title: Functional analysis of lipid acyl hydrolases in Arabidopsis antimicrobial defense: plp2 paraquat

status: Public on May 10 2009

city: EVRY CEDEX

first: Elftieh

last: Samira

address: 2 rue Gaston Crémieux, CP 5708

department: Unité de Recherche en Génomique Végétale

summary:
af13_plp2 - plp2 paraquat - Effects of deregulation of a lipid acyl hydrolase gene (PLP2, At2g26560) on global transcriptome upon infection by Botrytis cinerea. This deregulation affects resistance levels against fungal and bacterial pathogens, likely by perturbing the biosynthesis of oxylipins. Oxylipins are fatty acid-derived compounds (example:jasmonic acid) with diverse signaling or antimicrobial properties. - 10 uM Paraquat was infiltated in mesophyll of leaves with a syringe without needle. Leaf material was harvested at 0, 4 and 18 hours later. 3 plant genotypes were used (Col-0 ecotype) : - siPLP2 (RNAi-silenced) - pBIN (empty pBIN-transformed) - PLP2OE (PLP2-overexpressors).

Keywords: gene knock in (transgenic),time course


title: Plant cell wall and development. Comparison of transcript levels between elongating 5 and 11 day-old plants

status: Public on Mar 01 2009

city: evry

summary:
rs05-11_hypocotyls - hypocotyls - Fine regulation of genes specifically expressed during cell elongation. - Seeds of A. thaliana were sowed on culture medium poured in Magenta boxes. They were allowed to germinate. Plantlets were in vitro for 5 or 11 days and harvested for RNA extraction.

Keywords: organ comparison

first: Ludivine

last: Taconnat

first: Elisabeth

last: Jamet


title: Expression profiles in two early developmental stages of Sparus aurata

status: Public on Feb 20 2009

city: Legnaro

first: Luca

last: Bargelloni

state: PD

address: Viale dell'Università 16

department: Dept. Sanità Pubblica, Patologia Comparata ed Ig. Veterinaria

institute: Agripolis

summary: Two different early developmental stages of gilthead sea bream: i) larvae at 24 hours post-hatching ( Stage 1),  and ii) larvae at 96 hours post-hatching (Stage 4), were used for gene expression analysis. For each stage, total RNA was extracted from five (5) independent biological replicates, each consisting of pools of approximately 40-50 larvae. Based on SAM analysis, 1518 genes were differentially expressed between the two stages with a FDR (False Discovery Rate) of 0.0.

overall_design: In this study, we analyzed the gene expression profiles of two early developmental stages of gilthead sea bream using Agilent-016251 Sparus aurata Oligo Microarray platform (10 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays  are scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides are scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal .


title: ler vs pop2-1: gaba over-accumulation effects-Transcriptomic analysis of pop2-1 mutant in Arabidopsis thaliana

first: Agnes

last: Yu

summary:
au05-03_gaba - ler vs pop2-1: gaba over-accumulation effects - The analysis aims at identifying genes that are differentially regulated by the over-accumulation of GABA observed in the mutant pop2-1 in response to treatment with exogenous GABA and that may explain the singular phenotype of the mutant in this condition.
Designed experiment consisted in comparison of transcriptomes of Arabidopsis thaliana Landsberg erecta ecotype and its mutant pop2-1 (impaired in GABA transaminase activity) during a kinetic of endogenous GABA accumulation. For this purpose, 10-day-old plants grown on half strength Hoagland's agar medium were transferred to agar plates supplemented with 1 mM GABA. We isolated RNA from plants treated for 0, 1 and 4 days. Treatments were made in duplicate.
Keywords: gene knock-out, time course

sample_organism:
Populus x canadensis
Arabidopsis thaliana

first: Carole

last: DELEU


title: zip9_target_genes-Functional Characterization of AtbZIP9

summary:
au06-02_bzo2h - zip9_target_genes - Identify the target genes of the bZIP transcriptional regulator AtbZIP9 - three genotypes were grown in MS/2, 0,03% glicose (starvation) for 7 days under constant dim light. Three days dormancy break.
Keywords: gene knock in (transgenic),gene knock out

overall_design: 9 dye-swap - CATMA arrays

first: Michel

last: Vincentz


title: Functional analysis of lipid acyl hydrolases in Arabidopsis antimicrobial defense: plp2 Botrytis cinerea

summary: af13_plp2 - plp2 botrytis cinerea 2 - Effects of deregulation of a lipid acyl hydrolase gene (PLP2, At2g26560) on global transcriptome upon infection by Botrytis cinerea. This deregulation affects resistance levels against fungal and bacterial pathogens, likely by perturbing the biosynthesis of oxylipins. Oxylipins are fatty acid-derived compounds (example:jasmonic acid) with diverse signaling or antimicrobial properties. - 5000 spores of Botrytis were pipetted on 4 infection sites per ault leaf. Leaf material was harvested at 0 and 2 days later. 3 plant genotypes were used (Col-0 ecotype): siPLP2 (RNAi-silenced),pBIN (empty pBIN-transformed),PLP2OE (PLP2-overexpressors).

first: Samira

last: Elftieh


title: Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays

status: Public on Dec 06 2008

city: La Jolla

first: Samuel

last: Hazen

address: 9500 Gilman Drive

department: Cell and Developmental Biology

institute: University of California San Diego

type: Non-coding RNA profiling by genome tiling array

summary: A casual look at the behavior and function of animals and plants clearly shows that many physiological processes are periodic and tied to cyclical changes in a day.  As suggested by the persistence of some rhythms in the absence of external cues, organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock.  Transcription is an important mechanism in maintaining these oscillations.  Here we explore, using whole genome tiling arrays, the extent of rhythmic expression patterns genome wide, with an unbiased analysis of coding and noncoding regions of the Arabidopsis genome.  As in previous studies, we detected a circadian rhythm for approximately 25% of the protein coding genes in the genome.  With an unbiased interrogation of the genome, extensive rhythmic introns were detected predominantly in phase with adjacent rhythmic exons creating a transcript that if translated would be expected to produce a truncated protein.  In some cases such as the MYB transcription factor PHOSPATE STARVATION RESPONSE1, an intron was found to exhibit a circadian rhythm while the remainder of the transcript was otherwise arrhythmic.  In addition to several known non-coding transcripts including miRNA, trans-acting siRNA, and snoRNA, greater than one thousand intergenic regions were detected as circadian clock regulated, many of which have no predicted function, either coding or non-coding.  Nearly 7% of the protein coding genes produced rhythmic antisense transcripts, often for genes whose sense strand was not similarly rhythmic. This study revealed widespread circadian clock regulation of the Arabidopsis genome extending well beyond the protein coding transcripts measured to date.  This suggests a greater level of structural and temporal dynamics than previously known.

overall_design: Seedlings of Arabidopsis thaliana accession Col-0 were grown on MS media (supplemented with 2% D-glucose and solidified with 1% agar) 7 days in 12 h light:12 h dark cycles under white fluorescent bulbs at 100 mmol m-2 s-1 before release to constant light and temperature. Samples were collected every 4 h beginning at the time of lights on, ZT0.  Single perfect matches, without a 2nd partial match of >18/25 bp were selected giving a total of 1,683,620 unique features.  These were mapped to annotated mRNAs as intron, exon, inter-genic region, or flanking probes which span an annotated boundary. Hybridization efficiencies of oligonucleotide probes on tiling arrays vary considerably and some probes tend to be unresponsive.  Thus, to avoid spurious decrease of signal in the spectral analysis from poorly responsive probes, we filtered out probes which are lowly expressed (mean < 3) and furthermore show very little variation (standard deviation < 0.25) across the time series leaving a total of 1,609,258 features between both the forward and reverse strand arrays.  The twelve measurements for each probes were standardized and Fourier analysis was used to evaluate the RNA expression pattern over the two-day time course.  To exploit redundancy of features we grouped all probes for the same exon based on the TAIR7 genome annotation, or applied 200 bp windows centered on each intronic or intergenic probe position while stopping at exon boundaries.  We then computed the 24-h spectral power F24 from the average of the standardized probes within a group. To assess the significance of these F24 scores, we built empirical null distributions that take into account the number of probes (weight) that went into the calculation of the spectral power. The family of null distributions was calibrated from the distribution of scores of all probes annotated as intergenic. We parametrized these distributions as exponential functions which gave excellent fits. The p-values for all features were then computed from the fitted distributions.  The labeling method which used oligo dT for first strand amplification of the RNA produces a 3’ biased probes; therefore, any annotation unit with at least two features satisfying p < 0.005 was considered circadian regulated. For Fig. 2 the phases for genes were computed from the circular averages of the phase in individual exons using CIRCSTAT.

first: Felix

last: Naef

first: Tom

last: Quisel

first: Justin

middle: O

last: Borevitz

first: Joshua

last: Gendronq

first: Steve

last: Kay


title: Microarray analysis of the effects of ASP/MSH in melan-a melanocytes

status: Public on Feb 03 2009

city: Bethesda

first: Vincent

last: Hearing

address: Bldg 37  Rm 2132

department: National Cancer Institute

institute: National Institutes of Health

summary: We determined the gene expression profiles of murine melan-a melanocytes treated with ASP or alpha-MSH over a 4 days time course using genome-wide oligonucleotide microarrays. As expected, the gene expression patterns emphasized the opposing effects of the 2 ligands, and there were significant reductions in expression of numerous melanogenic proteins elicited by ASP, which correlates with its inhibition of pigmentation. However, ASP also unexpectidly modulated the expression of genes involved in various other cellular pathways, including glutathione synthesis and redox metabolism. Many genes up-regulated by ASP are involved in morphogenesis, cell adhesion and ECM-receptor interactions.

overall_design: Treatment with ASP or alpha-MSH was performed for 3 hr, 1 day, 2 days, 3 days and 4 days, in triplicate. Each biological replicate was submitted to a direct hybridization (treated/untreated samples) after coupling with Cy5 or Cy3 and to a reverse dye-swap, leading to 2 replicated hybridization for each biological sample. A total of 6 hybridized arrays was used for each of the 5 time points, for each drug.


title: Drosophila melanogaster developmental timecourse: wild type, eve, ftz

status: Public on Dec 31 2008

city: Chicago

first: Christopher

middle: David

last: Brown

department: Human Genetics

institute: University of Chicago

summary:
Transcriptional profiling of developmentally staged D. mel. Embryos for three genotypes: wild type, eve3 and ftz11
For additional information, please see Liu et al., 2009. Abstract: We constructed a large-scale functional network model in Drosophila melanogaster built around two key transcription factors involved in the process of embryonic segmentation.   Analysis of the model allowed the identification of a new role for the ubiquitin E3 ligase complex factor SPOP. In Drosophila, the gene encoding SPOP is a target of segmentation transcription factors.  Drosophila SPOP mediates degradation of the Jun-kinase phosphatase Puckered thereby inducing TNF/Eiger dependent apoptosis.  In humans we found that SPOP plays a conserved role in TNF-mediated JNK signaling and was highly expressed in 99% of clear cell renal cell carcinoma (RCC), the most prevalent form of kidney cancer. SPOP expression distinguished histological subtypes of RCC and facilitated identification of clear cell RCC as the primary tumor for metastatic lesions.

Keywords: 2 channel transcription timecourse

overall_design: Developmental timecourse, 3 genotypes, experimental sample vs. common reference.

middle: D


title: sqe1-Functional analysis and biotechnological application of genes involved in drought and salt stress tolerance

status: Public on Jan 24 2009

first: Soubigou-Taconnat

last: Ludivine

summary:
au07-13_sqe1 - sqe1 - Arabidopsis transcriptome microarray from wild type and mutant plants. - Arabidopsis microarray from Ler ecotype and the sqe-1 mutant.
Keywords: gene knock out

first: Jean-Pierre

last: Renou

first: Miguel

last: A. botella

first: Marie-Laure

last: Martin-Magniette


title: Technical replicates to determine array-to-array reproducibility.

first: Luca

last: Bargelloni

summary: Technical replicates, consisting of four independent hybridizations of the same labelled cRNA, were performed to determine array-to-array reproducibility. After normalization, correlation index between all replicates  exceeded 98%.

overall_design: In this study, we analyzed reproducibility of Agilent-016251  Sparus aurata Oligo Microarray based on single-colour detection (Cyanine-3 only). A RNA sample, prepared mixing four different larval stages of gilthead sea bream, was labelled in according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol. The same labelled cRNA was used for four independent fragmentation reactions and then hybridized spanning all array positions of 4x44K platform.  Microarrays  are scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides are scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended Background-Subtracted Signal.


title: hr-Transcriptomic analysis of the localized acquired resistance (LAR) phenomenon in Arabidopsis thaliana

status: Public on Dec 01 2008

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

summary:
tri38-lar - hr - Analyse the transcriptome of Arabidopsis thaliana plants developing localized acquired resistance (LAR) and a hypersensitive response (HR). The goal is to identify genes inducing LAR and/or HR. Here, we want to analyse the transcriptome of Arabidopsis thaliana developing HR. To achieve this, we used Col0 leaf tissues developing an HR reaction after inoculation of the avirulent strain of PstDC3000 carrying the gene avrRpm1.

Keywords: normal vs disease comparison

overall_design: 1 dye-swap - CATMA arrays

first: Serge-

last: KAUFFMANN


title: lar-Transcriptomic analysis of the localized acquired resistance (LAR) phenomenon in Arabidopsis thaliana

summary:
tri38-lar - lar - Analyse the transcriptome of Arabidopsis thaliana plants developing localized acquired resistance (LAR) and a hypersensitive response (HR). The goal is to identify genes inducing LAR and/or HR. Plants were treated either with PstDC3000 (avrRpm1)or MgCl2 (control plants). The samples were studied at 3 points of the infection kinetics of the LAR phenomenon: 6h, 24h and 48h.

Keywords: normal vs disease comparison

overall_design:
3 dye-swaps - CATMA arrays
12 biological repetitions were pooled for this experiment.


title: Characterization of the regulatory networks mediating TLR9 dependent gene activation in vivo

status: Public on Apr 01 2009

city: Frederick

first: Dennis

last: Klinman

department: CIP

summary:
CpG DNA interacts with TLR9 to stimulate a broadly protective innate immune response. This study uses bioinformatic network analysis of microarray data to identify the genes and regulatory networks triggered by CpG ODN. CpG treatment induced significant gene up-regulation (p < 0.00001) in the spleen within 30 min, peaking with the activation of >500 genes at 3 hr, and declining progressively thereafter. There were reproducible changes in the pattern of gene expression over time. This was mediated by a small group of “major inducers” (IL1A, IL1B, TNF, IFNG) whose activity was modulated by several “minor inducers” (NFKB1, IL6, IL15, IL18, STAT1, STAT2). The subsequent decline in gene activation was mediated by “suppressors” (MYC, IL1RN, SOCS1, SOCS3, NFKBIA, IL10, FOS) that actively down-regulated gene expression and targeted both major and minor inducers. Thus, the regulation of TLR9 dependent gene activation involves multiple waves of stimulation mediated by a small number of “major” and “minor” inducers followed by the active inhibition of gene expression by “suppressors”.
Keywords: time series design

overall_design: Endotoxin-free phosphorothioate ODN were synthesized at the CBER core facility (FDA, Bethesda, MD) as previously described. Mice were injected intraperitoneal (i.p.) with 400 ìg of an equimolar mixture of CpG ODNs 1555 (GCTAGACGTTAGCGT) and 1466 (TCAACGTTGA) or control ODNs 1612 (GCTAGATGTTAGCGT) and 1471 (TCAAGCTTGA). Spleens were surgically removed from mice under sterile conditions after 0.5, 1, 3, 9, 24 hr, and/or 72 hr, diced, and stored at -800 C in RNAlater (Qiagen, Valencia, CA). Data from 4 independent experiments/time point and 4-6 untreated controls were used for all statistical analyses. Reproducibility was established by comparing gene expression profiles among similarly treated mice from independent experiments in mAdb (referenced above). Expression analyses were performed using BRB ArrayTools (Biometric Research Branch, NCI). Data were background corrected, flagged values were removed, spots in which both signals were <100 were filtered out, ratios were log base 2 transformed and lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes (Yang et al., 2002). Analysis was restricted to genes present on >70% of the arrays after filtering. The gene expression profile of all treatment groups was compared to that of the control groups.


title: methotrexate treatment-dynamics of Arabidopsis transcriptome during folate depletion

status: Public on Dec 19 2008

first: Agnes

last: Yu

summary:
cea06-02_folate - methotrexate treatment - global analysis of the folate metabolism in Arabidopsis - Treatment of cells of Arabidopsis by methotrexate which is an inhibitor of the synthesis of the folate. Consequently, the pool of folates presents a strong reduction. The goal of this project is to look at the variations of expression in the Arabidopsis genome and specifically in some genes implied in the metabolism of the folate.
Keywords: time course,treated vs untreated comparison

overall_design: 10 dye-swap - CATMA arrays

first: Ravanel

last: Stephane


title: Mucosal Glycan Foraging Enhances the Fitness and Transmission of a Saccharolytic Human Distal Gut Symbiont: ECF mutant

status: Public on Nov 21 2008

city: Ann Arbor

first: Eric

last: Martens

summary: Growth of isogenic parent ('tdk strain'), 5xECF-sigma factor mutant and complemented mutant strain in the cecum of NMRI inbred mice fed a glycan-restricted, 'simple sugar' diet (35% each glucose and sucrose). Bacteria were collected from mouse distal gut 10 days after colonization.

overall_design: Experiment performed in biological triplicate; for purposes of cross-comparison, profiles were referenced to an in vitro minimal medium glucose chemostat culture (800ml volume, mid-log phase). Reference samples are GSM301635, 301637 and 301639 and are part of series GSE11944.

middle: C

first: Herbert

last: Chiang

first: Jeffrey

middle: I

last: Gordon


title: Knockdown of CD133 in melanoma cells

status: Public on Oct 16 2008

city: Zürich

first: Keith

last: Hoek

address: private

institute: Currently unaffilliated

summary: CD133 (Prominin-1) is considered the most important cancer stem cell (CSC)-associated marker identified so far, with increased expression in the CSC fraction of a large variety of human malignancies, including melanoma. Here we investigated the effects of CD133 down-regulation in vitro and in vivo in human metastatic melanoma. The average number of CD133 molecules on the cell surface of FEMX-I melanoma cells was decreased by 8.7-fold and 1.8-fold using two different short hairpin RNAs. Down-regulation of CD133, confirmed by immunocytochemistry, Western blotting, microarray analysis and RT-PCR, resulted in slower cell growth, reduced cell motility, and decreased capacity to form spheroids under stem cell-like growth conditions. Clonal analysis revealed that the reduction in growth rate was proportional to the extent of CD133 down-regulation. Monoclonal antibodies directed against two different epitopes of the CD133 protein induced a specific, dose-dependent cytotoxic effect in FEMX-I cells. The down-regulation of CD133 severely reduced the capacity of the cells to metastasize, particularly to the spinal cord. In the CD133 downregulated cells, microarray analysis revealed expression changes for only 143 annotated genes (76 up- and 67 down-regulated). Ten of the 76 up-regulated genes coded for Wnt inhibitors, suggesting an interaction between CD133 and the canonical Wnt pathway. We conclude that CD133, in addition to its role as a cancer stem cell marker, is an important therapeutic target for metastatic melanoma and, potentially, for other CD133-expressing cancer types.

overall_design: Two control experiments and two CD133 knockdown experiments.

first: Germana

last: Rappa

first: Oystein

last: Fodstad

first: Aurelio

last: Lorico


title: dgpp-DGPP regulated genes. Identification of diacylglycerol pyrophosphate regulated genes in ABA signaling.

status: Public on Oct 08 2008

first: Soubigou-Taconnat

last: Ludivine

summary:
rs05-06_dgpp - dgpp - The specific plant phosphorylated form of phosphatidic acid (PA), diacyglycerol pyrophosphate (DGPP) was recently shown to be a second messenger in abscisic acid (ABA) signaling. The aim of the project is to identify among the set of ABA-regulated genes the ones also regulated by DGPP and/or PA. - Five ml of 3 days-old suspension cells was incubated with ABA or lipids for 3 h under the conditions of culture. Lipids were emulsified by sonication for 1 mi, four times, at 4°C, in one ml of culture medium then added to 4 ml suspension cells. Cells were filtrated under vacuum, frozen in liquid nitrogen and RNA extracted. Dioleoyl PA and dioctanoyl PA are from Sigma, dioleoyl DGPP and dioctanoyl DGPP are from Avanti Polar Lipids.

Keywords: treated vs untreated comparison

first: Emmanuelle

last: Jeannette


title: arabidopsis ecotypes-Transcriptionnal response to potyviruses infection in Arabidopsis

status: Public on Oct 20 2008

summary:
ra06-05_potyvirus-ecotypes - arabidopsis ecotypes - Common and specific genes deregulated in response to various potyviruses in different Arabidopsis genetic backgrounds. - Four different Arabidopsis ecotypes were inoculated with one Potyviruse. About 4 weeks after sowing, the 6 expanded leaves plants were inoculated with the different viruses or were mock-inoculated. Seven days after inoculation, inoculated leaves were collected, RNA was extracted and virus infection controlled. RNA fron infected plants was then used for microarrays hybridization. Three biological repeat have been done and two dye-swap.
Keywords: normal vs disease comparison

first: Jean-Pierre

last: Renou

first: Valerie

last: Schurdi-Levraud


title: potyvirus effect-Transcriptionnal response to potyviruses infection in Arabidopsis

summary:
ra06-05_potyvirus-ecotypes - potyvirus effect - Common and specific genes deregulated in response to various potyviruses in different Arabidopsis genetic backgrounds. - Arabidopsis thaliana ecotype Ler was inoculated with three different Potyviruses. About 4 weeks after sowing, the 6 expanded leaves plants were inoculated with the different viruses or were mock-inoculated. Seven days after inoculation, inoculated leaves were collected, RNA was extracted and virus infection controlled. Three biological repeats have been done and two dye-swaps.
Keywords: normal vs disease comparison

first: Marie-Laure

last: Martin-Magniette


title: Array-based miRNA Profiling of Clear Cell Renal Cell Cancer

status: Public on Oct 01 2008

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: MicroRNAs (miRNAs) are short single stranded RNAs that are associated with gene regulation at the transcriptional and translational level. Changes in their expression were found in a variety of human cancers. Because of the lack of corresponding data in clear renal cell carcinoma (ccRCC) we have performed genome-wide expression profiling of miRNAs using microarray analysis and quantification of specific miRNAs by TaqMan real-time RT-PCR. Matched malignant and non-malignant tissue samples from two independent 12 ccRCC sets were profiled. The microassay-based experiments identified 14 overexpressed and 20 downregultaed miRNAs in malignant samples. Expression in ccRCC tissue samples compared to matched non-malignant samples measured by RT-PCR was increased by 2.7 to 28fold for the hsa-mir-16, -452, -224, -155, and -210, but decreased by 6.2 to 96fold for hsa-mir-200b, -363, , -429, -200c, -514, and -141. No significant associations between these differentially expressed miRNAs and the clinico-pathological factors tumor stage, grade, and survival rate were found.  Nevertheless, malignant and non-malignant tissue could clearly be differentiated by their miRNA profile . A combination of miR-141 and miR-155 resulted in a 96% overall correct classification of samples. The presented differential miRNA pattern provides a solid basis for further validation including functional studies.

overall_design: The study was performed with two independent sample sets. For each set 12 kidney tissue sample pairs were derived from adult patients undergoing radical nephrectomy at the University Hospital Charité. All tumor types were clear renal cell carcinoma. Tumor classification and stage were established according to the 2002 TNM System and the 2004 WHO Classification. Matched malignant (#NC (e.g. 2NC)) and non-malignant  (#NN (e.g. 1NN)) tissue samples from two independent 12 ccRCC sets were profiled.

first: Mollenkopf

last: Hans-Joachim

first: Jung

last: Klaus

last: Monika

first: Kristiansen

last: Glenn


title: crc1 mutant-Modelling the Transcriptional Network in Arabidopsis Fruit Development.

status: Public on Sep 25 2008

first: Frederique

last: Bitton

institute: INRA

summary:
gen45-carpel_development - crc1 mutant - Identification of target genes from three transcription factors involved in gynoecium development - Comparison between the wild type Ler and crc1 mutant.

Keywords: gene knock out

first: Charles

last: Scutt


title: dgpp-2 DGPP-regulated genes: Identification of diacylglycerol pyrophosphate-regulated genes in ABA signaling

status: Public on Sep 27 2008

summary: rs05-06_dgpp - dgpp - 2.  The specific plant phosphorylated form of phosphatidic acid (PA), diacyglycerol pyrophosphate (DGPP), was recently shown to be a second messenger in abscisic acid (ABA) signaling. The aim of the project is to identify among the set of ABA-regulated genes the ones also regulated by DGPP and/or PA.

overall_design:
4 dye-swap - CATMA arrays
5ml of 3 days-old suspension cells were incubated with ABA or DGPP 18:1 for 3hours under the conditions of culture. DGPP was emulsified by sonication for 1min 4 times at 4°C in 1ml of culture medium then added to 4ml of suspension cells. Cells were filtrated under vacuum, frozen in liquid nitrogen and RNA extracted. DGPP is from Avanti Polar Lipids.

first: Ludivine

last: Taconnat


title: Wild type mice (Trsp) vs Trsp-knockout mice (DTrsp) or A34 or G37L or G37H transgenic mice

status: Public on Aug 19 2008

first: Dolph

last: Hatfield

address: 37 Convent Drive, Rm. 6032A

summary:
Comparative analysis of gene expression in the liver of the Trsp-knockout mice  (Trspfl/fl-AlbCre+/+) and A34 (Trspfl/fl-AlbCre+/+-A34t/t), G37L (Trspfl/fl-AlbCre+/+-G37t/t; 2 copies), G37H (Trspfl/fl-AlbCre+/+-G37t/t; 16 copies) transgenic mice with gene expression of wild type mice (Trsp+/+-AlbCre+/+).

Sec (selenocysteine) is biosynthesized on its tRNA and incorporated into selenium-containing proteins (selenoproteins) as the 21st amino acid residue. Selenoprotein synthesis is dependent on Sec tRNA and the expression of this class of proteins can be modulated by altering Sec tRNA expression. The gene encoding Sec tRNA (Trsp) is a single-copy gene and its targeted removal in liver demonstrated that selenoproteins are essential for proper function wherein their absence leads to necrosis and hepatocellular degeneration. In the present study, we found that the complete loss of selenoproteins in liver was compensated for by an enhanced expression of several phase II response genes and their corresponding gene products. The replacement of selenoprotein synthesis in mice carrying mutant Trsp transgenes, wherein housekeeping, but not stress-related selenoproteins are expressed, led to normal expression of phase II response genes. Thus the present study provides evidence for a functional link between housekeeping selenoproteins and phase II enzymes.

overall_design: Trsp vs DTrsp; Trsp vs A34; Trsp vs G37L; Trsp vs G37H. Biological replicates from littermates. One replicate per array.

first: Aniruddha

last: Sengupta

first: Bradley

last: Carlson

first: James

last: Weaver

first: Sergey

middle: V

last: Novoselov

first: Dmitri

middle: E

last: Fomenko

first: Vadim

last: Gladyshev


title: drought and salt stress response-Eskimo gene characterisation.

status: Public on Sep 11 2008

first: Agnes

last: Yu

summary:
ra06-02_staygreen - drought and salt stress response - Modification of the transcriptome by the eskimo mutation and response to stress. - Individual plants were grown in Fertiss clods in a culture chamber. 3 treatments were made to the plants : control, drought and salt.
Keywords: gene knock out,treated vs untreated comparison

overall_design: 6 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Mylene

last: Durand-Tardif

first: Fabienne

last: Granier