title: The use of Microarray Technology to screen for immune related genes regulated during infection with Avibacterium paragallinarum serovar C-3

status: Public on May 03 2013

city: Bloemfontein

first: Charlotte

last: Boucher

state: Free State

address: Nelson Mandela Drive

department: Microbial, Biochemical and Food Biotechnology

country: South Africa

institute: University of the Free State

summary: Avibacterium paragallinarum is the causative agent of Infectious Coryza, an acute upper respiratory tract disease in chickens. The occurrence of outbreaks has emphasized that the disease can be significant in broiler as well as layer chickens. In developing countries, infectious coryza is commonly complicated by a range of other infections, resulting in severe disease and significant economic losses. There are vaccines on the market but with limited efficiency, due to the serological differences amongst the different serogroups of A. paragallinarum. Recent advances in genomics have led to whole genome sequencing of the chicken, creating an opportunity for the use of high-throughput technology such as microarrays. The objectives of this study was to screen for gene expression patterns across clinical scores associated with the immune response in chickens infected with A. paragallinarum serovar C3, as well as to establish which biological pathways are stumulated when infected with A. paragallinarum.

overall_design: A total of 15 birds (male, leghorn) were obtained at 10 weeks of age. The birds were kept in separate layer cages up until 21 weeks, this is the susceptible age for infectious coryza. Twelve (12) birds were challenged via the infra-orbital eye area with 0.1ml challenge bacterium (A.paragallinarum serovar C3), Three were left unchallenged, which served as the control. As symptoms developed birds were scored, with score1 representing mild symptoms, score2, moderate and score3 representing severe symptoms. Each score is represented by two biological replicates. Thus a total of 8 samples were hybridized, two representing control.

middle: E

first: Robert

last: Bragg


title: Genes array from human mesenchymal stem cells (hMSCs) with knockdown EZH2

status: Public on Dec 05 2012

city: Taichung

first: chanshiou

last: Wu

address: No6,Hsueh-shih road

country: Taiwan

institute: china medical university

summary:
EZH2 plays an important role in stem cell renewal and maintenance by inducing gene silencing via its histone methyltransferase activity.
EZH2 downregulation markedly enhances neuron differentiation of human mesenchymal stem cells (hMSCs)chromatin at promoters of EZH2 target genes.

overall_design: comparison of knockdown EZH2 of hMSCs vs hMSCs

first: Yung-Luen

last: Yu

first: Chen-Shiou


title: Expression analysis of Gordonia sp. KTR9 upon exposure to RDX and Nitrogen limitation

status: Public on Feb 06 2013

city: Vicksburg

first: Dawn

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

country: USA

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

summary:
Investigation of gene expression level changes in Gordonia sp. KTR9 upon exposure to RDX and Nitrogen Limitation, compared to controls with no RDX.
The Gordonia sp. KTR9 strain used in this study has been previously described by Thompson KT, Crocker FH, Fredrickson HL.2005. Mineralization of the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine by Gordonia and Williamsia spp. Appl Environ Microbiol. 2005 Dec;71(12):8265-72.

overall_design: A 12 x 135K array study using total RNA recovered from triplicate cultures of KTR9 exposed to RDX, triplicate cultures of KTR9 exposed to RDX and high nitrogen conditions, triplicate cultures of KTR9 exposed to low nitrogen, and triplicate cultures of controls exposed to high nitrogen.

first: Karl

middle: J

last: Indest


title: Expression analysis of Gordonia sp. KTR9 and Gordonia sp. KTR9 mutant GlnR upon exposure to high and low Nitrogen conditions

summary:
Investigation of gene expression level changes in Gordonia sp. KTR9 and Gordonia sp. KTR9 mutant GlnR upon exposure to high and low nitrogen conditions
The Gordonia sp. KTR9 strain used in this study has been previously described by Thompson KT, Crocker FH, Fredrickson HL.2005. Mineralization of the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine by Gordonia and Williamsia spp. Appl Environ Microbiol. 2005 Dec;71(12):8265-72.

overall_design: A 12 x 135K array study using total RNA recovered from triplicate cultures of KTR9 exposed to high nitrogen conditions, triplicate cultures of KTR9 exposed to low nitrogen conditions, triplicate cultures of KTR9 mutant GlnR exposed to high nitrogen conditions, triplicate cultures of KTR9 mutant GlnR exposed to low nitrogen conditions.


title: RDX degradation studies with KTR9 GntR knockout

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Targeted inhibition of human breast cancer cell lines selected as model systems of ERBB2-positive/EGFR high breast cancer

status: Public on Oct 22 2012

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

country: Germany

institute: German Cancer Research Center


title: Human primary airway epithelial cell cultures infected with human- and swine-origin influenza viruses

status: Public on Oct 11 2012

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary: Cultures of primary human airway epithelial cells (HAE cells) were exposed to an MDCK equivalent MOI of 0.01 of several swine- and human-origin influenza viruses and RNA was extracted at the 12, 16, and 24 hours post infection.

overall_design: 64 samples consiting of 5 influenza strains, 3 time points and 2 or 3 replicates at each time point. Expression of mock-infected samples measured at each time point.

first: Alan

last: Aderem


title: Targeted inhibition of human breast cancer cell lines selected as model systems of ERBB2-positive/EGFR high breast cancer [RPPA-HCC1954]

summary:
EGFR-inhibition is required for targeted therapies of ERBB2-positive/EGFR high breast cancer.
Approximately 30% of human ERBB2-positive breast tumors also express EGFR.

overall_design: Three targeted therapeutics (erlotinib, pertuzumab, trastuzumab) and two ligands (EGF, HRG) were analyzed in all possible combinations. Each experiment involving inhibition with targeted drugs was performed in three, and measurements without inhibitors were performed in five biological replicates. This resulted in 780 samples. Incubation with therapeutics only and dilution series of control lysated were included as controls.

first: Frauke

last: Henjes

first: Christian

last: Bender

first: Silvia

last: von der Heyde

first: Lisa

last: Braun

first: Heiko

middle: A

last: Mannsperger

last: Schmidt

first: Stefan

last: Wiemann

first: Max

last: Hasmann

first: Sebastian

last: Aulmann

first: Tim

last: Beissbarth


title: Targeted inhibition of human breast cancer cell lines selected as model systems of ERBB2-positive/EGFR high breast cancer [RPPA-SKBR3]

overall_design: Three targeted therapeutics (erlotinib, pertuzumab, trastuzumab) and two ligands (EGF, HRG) were analyzed in all possible combinations. Each experiment involving inhibition with targeted drugs was performed in three, and measurements without inhibitors were performed in five biological replicates. This resulted in 780 samples. HRG stimulated cells under the triple drug combination exceptionally have two biological replicates. Incubation with therapeutics only and dilution series of control lysated were included as controls.


title: In vitro transcriptional profiling of Bacteroides fragilis in glucose and human milk oligosaccharides

status: Public on Sep 30 2012

city: Davis

first: Bart

middle: C.

last: Weimer

state: CA

address: 1 Shields Ave

department: Population Health and Reproduction

institute: University of California, Davis

summary: The factors that govern the retention and abundance of specific microbial lineages within a developing intestinal microbiota remain poorly defined. Human milk oligosaccharides consumed by nursing infnats pass undigested to the distal gut where they may be consumed by microbes. We investigated the transcriptional response of Bacterides fragilis, a prominent gut resident, to the presence of HMOs.

overall_design: In vitro transcriptional profiles of Bacteroides fragilis obtained from biological duplicate cultures taken at middle log phase in minimal media glucose (MM-Glu) and in minimal media with human milk oligosaccharides (MM-HMO).


title: The effect of underfeeding on gene expression in the bovine tract during postpartum

status: Public on Jul 31 2012

city: Jouy en Josas

first: Isabelle

last: Hue

address: Domaine de Vilvert

department: PHASE

country: France

institute: INRA

summary: This study aimed to investigate the effect of a mild underfeeding on global gene expression in the oviduct, the endometrium and the corpus luteum between 4 and 15 days post-ovulation in postpartum (PP) Holstein cows. Four control cows (C) received 100% of energy and protein requirements after calving when 4 underfed (U) received 80% of the control diet. Oestrus synchronization treatment was applied to induce ovulation on D80 PP. Oviduct, ovaries and the anterior part of each uterine horn were recovered chirurgically 4, 8, 12 and 15 days after ovulation. Gene expression was assessed on a dedicated 10K array and statistically analyzed on pools across the oestrus cycle days. Tissues appeared divergently "diet-responsive" as no differentially expressed gene (DEG) in the corpus luteum between U and C were highlighted, conversely to 293 DEGs in the oviduct vs. 1 in endometrium under a False discovery rate (FDR)<0.11, and 3830 DEGs vs. 28 respectively under a FDR<0.30. Pathways involved immunity, lipid catabolism and cell proliferation. However, once correlated with dedicated statistics (regularized canonical correlation analysis) to the evolution of 6 plasmatic markers measured weekly over 80 days, IGF-1, insulin, beta-Hydroxybutyrate and genes potentially implied in tissue repair mechanisms (e.g. FABP5/CRABP2, ELF1, TCEA1, NF-kB, TGF-beta1, HNF4A) became relevant to dairy cow physiology during PP in the oviduct and the endometrium. Keywords: Postpartum dairy cows, induced cycle, mild underfeeding, genital tract, gene-metabolites correlations

overall_design: Total RNA from each tissue (endometrium, corpus luteum, oviduct) were indirectly labelled using "random" hexamers. One independent target per tissue and per diet was generated and hybridised onto one array. 4 measurements per diet were generated.

first: Damien

last: Valour

first: Séverine

last: Degrelle

first: Sébastien

last: Déjean

first: Guillemette

last: Marot

first: Olivier

last: Dubois

first: Guy

last: Germain

first: Patrice

last: Humblot

first: Andrew

last: Ponter

first: Gilles

last: Charpigny

first: Bénédicte

last: Grimard


title: Pancreatic Cancer HPAF/CD18 cells: Ecd knockdown vs Scrambled

status: Public on Aug 10 2012

city: Omaha

first: Parama

last: Dey

state: Nebraska

address: 985870 Nebraska Medical Center

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

summary:
Purpose: To study the expression and function of a novel cell cycle regulatory protein, human ecdysoneless (Ecd), during pancreatic cancer (PC) pathogenesis.
Experimental Design: Immunohistochemical expression profiling of Ecd was done in non-neoplastic normal pancreatic tissues and pancreatic ductal adenocarcinoma lesions (from tissue microarray and Rapid Autopsy program) as well as precancerous PanIN lesions and metastatic organs. To analyze the biological significance of Ecd in PC progression, Ecd was stably knocked down in PC cell line followed by in vitro and in vivo functional assays.
Results: Normal pancreatic ducts show very weak to no Ecd expression compared to significant positive expression in PC tissues (mean±SE composite score: 0.3±0.2 and 3.8±0.2 respectively, p<0.0001) as well as in PanIN precursor lesions with a progressive increase in Ecd expression with increasing dysplasia (PanIN-1 to PanIN-3). Analysis of matched primary tumors and metastases from PC patients revealed that Ecd is highly expressed in both primary pancreatic tumor and in distant metastatic sites. Further, knockdown of Ecd suppressed cell proliferation in vitro and tumorigenicity of PC cells in mice orthotopic tumors. Microarray study revealed that Ecd regulates expression of glucose transporter GLUT4 in PC cells and was subsequently shown to modulate glucose uptake, lactate production and ATP generation by PC cells. Finally, knockdown of Ecd also reduced level of pAkt, key signaling molecule known to regulate aerobic glycolysis in cancer cells.
Conclusion: Ecd is a novel tumor promoting factor that is differentially expressed in pancreatic cancer and potentially regulates glucose metabolism within cancer cells.

overall_design: Two-condition experiment, Ecd knockdown vs Scrambled cells. Biological replicates: 3 Ecd knockdownl, 3 Scrambled, independently grown and harvested. One replicate per array

last: Deya

first: Satyanarayana

last: Rachagania

first: Subhankar

last: Chakrabortya

first: Pankaj

middle: K

last: Singhd

first: Xiangshan

last: Zhaob

first: Channabasavaiah

last: Basavaraju Gurumurthyb

first: Judy

middle: M

last: Andersond

first: Subodh

last: Lelec

first: Michael

last: Hollingsworthd

first: Vimla

last: Bandb

first: Surinder

last: Batraa


title: Targeted inhibition of human breast cancer cell lines selected as model systems of ERBB2-positive/EGFR high breast cancer [RPPA-Longterm]

first: Ulrike

last: Korf

summary:
EGFR-inhibition is required for targeted therapies of EGFR high/ERBB2 positive breast cancer.
Approximately 30% of human ERBB2 positive breast tumors also express EGFR.

overall_design: Three therapeutics were analyzed in five combinations plus control. Each experiment was performed in three biological replicates. This resulted in 180 samples. Exceptionally, time point 18 has just two biological replicates, and time point 48 just one. A dilution series of control lysated was included as control.

first: Frauke

last: Henjes

first: Christian

last: Bender

first: Silvia

last: von der Heyde

first: Lisa

last: Braun

first: Heiko

last: Mannsperger

last: Schmidt

first: Stefan

last: Wiemann

first: Max

last: Hasmann

first: Sebastian

last: Aulmann

first: Tim

last: Beissbarth


title: Effect of c-MET inhibitor SU11274 upon sensitive (RPMI8226) or multi-resistant (RPMI8226/R5) Multiple Myeloma cell lines

status: Public on May 25 2012

city: Bari

first: angelina

last: boccarelli

state: Bari

address: P.zza G. Cesare, 11

department: Department of Biomedical Sciences and Human Oncology

country: Italy

institute: University of Bari

summary: The c-MET signaling axis is increasingly implicated in tumorigenesis and chemioresistance. In this study, we investigated gene expression modifications induced by SU11274 (Selleck Chemicals, Boston, USA), a novel selective c-MET inhibitor, in a pair of isogenic multiple myeloma (MM) cell lines either sensitive (RPMI8226) or multi-resistant, highly c-MET expressing (RPMI8226/R5) cells.  On the whole, RPMI8226/R5 cells after SU11274 were characterised by wider and diverse gene expression modifications than RPMI8226, indicating that c-MET over-expression, and its inhibition, is an important aspect of the adaptive response associated to drug resistance.

overall_design: RPMI8226 and RPMI8226/R5 cells are cultured in RPMI 1640 supplemented with10% fetal calf serum (FCS), 100U/ml penicillin and streptomicin (Euroclone UK) and 1mM Hepes buffer at 37 °C in a humified 5% CO2 atmosphere. The effect of SU11274 on gene expression of both cell lines was evaluated in three distinct experiments. 500,000 cells/ml in T25 flasks were treated with SU11274 (10 µM final concentration) or vehicle, for 6 h at 37 °C. At the end of the incubation time, treated and control untreated cells were washed and resuspended for RNA extraction. Linear mRNA amplification and labeling of fluorescent cDNA targets (Cy5, treated sample, Cy3, untreated sample) were performed using the Amino Allyl aRNA Amplification MessageAmp II Kit (Ambion), and examined Phalanx Human OneArray HOA (Phalanx Biotech Group's ) microarrays. Array scanning was carried out using a ChipReader VersArray ® 5 micron dual confocal laser scanner with VersArray ChipReader v3.1 analysis software, while the images were analyzed by scanner row VersArray Analyzer v4.5 software (Bio-Rad Laboratories) with intensity average pixels for each spot. Global Fund has been removed from biquadratic polynomial and the normalization of multiple channels was carried out by local regression (loess), the logarithmic transformation was then performed for each level of expression.

first: Angelina

last: Boccarelli


title: Dietary alleviation of maternal obesity and diabetes: increased resistance to diet-induced obesity transcriptional and epigenetic signatures

status: Public on Apr 01 2012

city: Paris

first: Jean-Philippe

last: Jais

address: 149 rue de Sevres

institute: Université Paris Descartes - Hopital Necker-Enfants Malades

summary: We have previously reported that providing a control diet to obese and diabetic mice during the periconceptional/gestation/lactation period, led to a drastic sex-specific shift from susceptibility to resistance to high fat feeding (HFD) in the female offspring. In the present study, we aimed to characterize exhaustively the metabolic phenotype of  F1 and F2 sensitive (S1, S2) and resistant (R1, R2) mice and underscore in the liver, muscle and adipose tissue, the transcriptional and epigenetic mechanisms supporting the response to HFD, the trait of resistance/susceptibility and the adaptation across generations. We report the transcriptomic analyses realized based on a candidate gene approach in the liver using a custom mouse microchip.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: A direct comparison strategy with dye-swapping was used to compare two conditions and dye-swaps were replicated several times with at least 4 different animals/group. The comparisons of primary interest: S1 vs N1 (S1/N1); S2 vs N2 (S2/N2); R2 vs N2 (R2/N2); R2 vs S2 (R2/S2) and S2 vs S1 (S2/S1) were made according to a design such that secondary comparisons could be estimated.

first: Linda

last: Attig

first: Alexandre

last: Vigé

first: Moshen

last: Karimi

first: Aurore

last: Beauger

first: Marie-Sylvie

last: Gross

first: Anne

last: Athias

first: Catherine

last: Gallou-Kabani

first: Philippe

last: Gambert

first: Tomas

last: Ekstrom

first: Claudine

last: Junien


title: A new genome wide expression array and its application to eQTL mapping, synergy to other platforms

status: Public on Apr 30 2012

city: Hsinchu

first: Li-Lan

last: Li

address: 195,Sec. 4, Chung Hsing Rd. Chutung

summary: The study of gene expression as an intermediate phenotype in associating genotype to disease is growing rapidly. The success of this approach depends heavily on the availability of accurate, high throughput platforms for assaying expression levels of genome-wide gene sets. We evaluated a new platform for gene expression, Phalanx Human OneArray (HOA), in 90 HapMap cell lines (CEU panel) for which Illumina BeadChip data were available (Stranger et al. 2007, PMID: 17873874). We found high reproducibility between technical HOA replicates (R = 0.99) and strong inter-platform correlation based on 2,458 sequence-matched probes (R = 0.87). We next performed an association analysis between gene expression levels and HapMap SNPs in the 60 unrelated CEU parents [SNP data downloaded directly from HapMap project (http://www.hapmap.org/)(HapMap phase II/Rel # 22)]. Among the 4356 genes (HOA array) showing variable expression, 122 (2.8%) had a significant cis association (p-value < 0.001) with at least one SNP. Of the 1751 genes showing variable expression on both platforms, 84 had a significant cis association with 36.9% of the genes (31/84) present in both data sets, 39.3 % (33/84) only in HOA, and 23.8% (20/84) only in Illumina. A subset of these 84 eQTLs overlap or are in strong linkage disequilibrium (LD) with reported complex disease/trait susceptibility loci. Combining the results of the two platforms provides a more comprehensive eQTL database (30% increase), which may help to accelerate our understanding of the molecular basis of quantitative traits and diseases.

overall_design:
We quantified gene expression levels in the 90 HapMap cell lines (CEU panel) using Phalanx HOA for which Illumina BeadChip data were available (Stranger et al. 2007). We used the same set of RNA samples employed in Stranger et al 2007 (see GEO Series GSE6536, CEU panel; raw data were re-analyzed, ie, re-normalized, thereby generating new values) which allowed us to undertake a detailed comparison to the Illumina expression platform and profiled the 60 parent samples at Industrial Technology Research Institute (ITRI), Taiwan and the 30 children samples at Wellcome Trust Sanger Institute (WTSI), United Kingdom. We performed two in vitro transcription (IVT) reactions for each RNA sample and three technical replicates per IVT with exception of seven samples (15CP, 33CP, 43CP, 44CP, 48CP, 56CP, 60CP) that had two technical replicates for one of the two IVT reactions.

*** This Series represents the Phalanx HOA data. ***

File "info.pass.parent.txt" (a description of the relationship between an array and a sample and its replicates) is linked below as a supplementary file.

first: Shu-Hui

last: Sheng

first: Tai-Been

last: Chen

first: Albus

last: Pai

first: Chiuan-Huei

last: Wang

first: Yen-Ju

last: Lin

first: Henry

middle: H

last: Lu

first: Barbara

last: Stranger

first: Emmanouil

middle: T

last: Dermitzakis

first: Panagiotis

last: Deloukas


title: affy_cotton_2011_12 - Comparative transcriptional profiling of cotton fibers in Gossypium hirsutum and Gossypium barbadense using EST pyrosequencing and microarray hybridization

status: Public on Oct 03 2012

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary: affy_cotton_2011_12 - affy_cotton_2011_12 - In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs. As a complementary approach, we conducted microarray-based hybridization profiling using the cotton Affymetrix gene chip and labeled cDNAs from fibers at 11 dpa and for the same two genotypes and compared differentially expressed genes identified by the two platforms. The 454 unigenes were also mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.-Total RNA was extracted from 11 dpa-old fibers from the two genotypes, Guazuncho 2 (Gossypium hirsutum) and VH8-4602 (G. barbadense), and included two replicates of each. RNA was checked for quality and quantity using an Agilent Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA, http://www.home.agilent.com) following the manufacturer’s recommendations. The RNA was sent to the Australian Genome Research Facility Ltd. (http://www.agrf.org.au, Melbourne, Victoria, Australia) for labeling and hybridization to the Affymetrix Genechip® Cotton Genome Array (21,854 genes) (Affymetrix, http://www.affymetrix.com/). -

sample_organism:
Gossypium barbadense
Gossypium hirsutum

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design:
4 arrays - Cotton; x comparison between two genotypes in cell type

This represents the gene expression component of the study only

first: Thierry

last: Lagrange

first: Stephanie

last: Huguet

first: Danny

last: Llewellyn

first: Jean-Marc

last: Lacape

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Cumulus cells genetic profile of patients stimulated with r-hLH or hCG evaluated with MicroArray analysis versus r-hFSH stimulated COCs

status: Public on Jun 28 2012

city: Chieti

first: Valentina

last: Gatta

state: Abruzzo

address: Via Colle dell'Ara

department: Aging Research Center (CESI)

institute: G. d’Annunzio University Foundation Chieti

summary: The aim of this study was to evaluate if different ovaric stimulation protocols modify gene expression profiles in COCs of infertile women. mRNA pools in COCs are essential for correct meiosis and activation of oocyte during fecondation and their alterations lead to reduced differentiation and oocyte functionality. In particular we tested the action of 2 different stimulation protocol on COCs transcriptome by MicroArray analysis of COCs after stimulation with r-hLH or h-CG versus COCs stimulated with r-hFSH. We identified genes and networks selectively altered after the different treatment protocols involved in proliferation and activity of COCs.

overall_design: The study was based on MicroArray analysis of COCs obtained from infertile women after ovaric stimulation. We performed a total of 6 experiments using COCs pools from each woman. 4 experiments were biological replicates and 2 were dye swaps replicates.

first: Marco

last: D'Aurora

first: Sara

last: Franchi

first: Samantha

last: Sperduti

first: Liborio

last: Stuppia

first: Carla

last: Tatone

first: Paolo

last: Artini

first: Rosanna

last: Ciriminna

first: Mariaelena

last: Vento


title: Transcript map of Shewanella oneidensis MR-1

status: Public on Jul 19 2012

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

type: Expression profiling by genome tiling array

summary: High-resolution tiling analysis of the MR-1  transcriptome in defined lactate minimal medium

overall_design: One slide hybridized to mRNA and one “genomic control” array hybridized to genomic DNA

first: Wenjun

last: Shao

first: Adam

last: Deutschbauer

middle: P

last: Arkin


title: wt dex induction-Establishing the network of seed gene expression and analysis of its biodiversity

status: Public on Mar 27 2012

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

summary: tri33-lec1 - wt dex induction - Identification of LEC1 target genes         - Induction of 14 days old WT seedlings , different treatments ( EtOH, DEX induction) for 8 hours

overall_design: 2 dye-swap - treated vs untreated comparison

first: Junker

last: Astrid


title: Expression data from juvenile Xenopus laevis inner ear tissue

status: Public on May 05 2012

city: Las Cruces

first: Elba

middle: E.

last: Serrano

address: 1200 S. Horseshoe, MSC 3AF

department: Biology

institute: New Mexico State University

summary:
We implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis.
Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear.

overall_design: Gene expression analysis of Xenopus laevis juvenile inner ear tissue.  Inner ear RNA isolated from three groups of 5-10 juvenile X. laevis. Each biological replicate represents pooled inner ear RNA from 10-19 inner ears.

first: TuShun

middle: R

last: Powers

first: Selene

last: Virk

first: Casilda

last: Trujillo-Provencio


title: Aberrantly expressed genes in HaCaT keratinocytes chronically exposed to arsenic trioxide

status: Public on Apr 12 2012

city: Jackson

first: udensi

middle: kalu

last: udensi

address: 1400 J R Lynch

institute: Jackson State University

summary:
The purpose of this study is to search for aberrant genes in HaCaT keratinocytes after chronic exposure to arsenic trioxide.
The objective of the investigation was to discover the mechanism of arsenic carcinogenicity in human epidermal keratinocytes. We hypothesize that a combined strategy of DNA microarray, qRT-PCR and gene function annotation will identify aberrantly expressed genes in HaCaT keratinocyte cell line after chronic treatment with arsenic trioxide. HaCaT cells were chronically exposed to 0.5µg/mL arsenic trioxide (As2O3) up to 22 passages and RNA was extracted. Microarray data analysis identified 14 up-regulated genes and 21 down-regulated genes in response to arsenic trioxide

overall_design: Two experimental groups: 1. The treatment group was sub-cultured up to passage 22 to establish a chronic exposure state. 2. The passage control group was also sub-cultured up to 22 passages but with no exposure to arsenic trioxide. 4 technical replicates with 3 replicates making a total of 8X3 =24 samples HaCat Cell untreated (passage control): 1. H1_H001, H1_H002, H1_H003 2. H2_ H004, H2_H005, H2_H006 3. H3_ H007, H3_H008, H3_H009 4. H4_ H010, H4_H011, H4_H012 HaCat Cell treated with 0.5µg/ml of arsenic trioxide: 5. A1_H013, A1_H014, A1_H015 6. A2_H016, A2_H017, A2_H018 7. A3_H019, A3_H020, A3_H021 8. A4_H022, A4_H023, A4_H024 Cell Type: Human Skin Keratinocyte: 1.5 ×105 HaCaT cells were cultured in 7.5 ml of complete DMEM containing 10% Fetal Bovine Serum (FBS) and 1% penicillin, streptomycin in T-25 culture plate. Cells were incubated in a humidified atmosphere with 5% CO2 at 37 ºC. The treatment groups were exposed to 0.5µg/mL As2O3 (equivalent to LC 0.5), and passaged at 90% confluent. Total RNA was extracted from 4 technical replicates of unexposed HaCaT cells and HaCaT cells chronically exposed to arsenic trioxide up to passage 22 using RNA STAT-60 (TEL-TEST, INC, Friendswood, TX, USA).

first: Udensi

last: Udensi

first: Raphael

middle: D

last: Isokpehi


title: Activation of STAT6 by STING Is Critical for Antiviral Innate Immunity

status: Public on Nov 21 2011

city: Beijing

first: Zhengfan

last: Jiang

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Sciences

country: China

institute: Peking University

summary: Analysis of the transcriptional response of HEK293 or HEK293-STAT6 stable cell lines to poly(I:C) transfection. The hypothesis tested was that poly(I:C) transfection is capable of inducing the expression of STAT6-dependent antiviral genes.

overall_design: mRNA isolated from HEK293 or HEK293-STAT6 stable cell lines with control treatment or poly(I:C) transfection for 16 hours.

first: Huihui

last: Chen


title: nitrate induction - nlp mutants-Nitrate induction - nlp mutants

status: Public on Dec 01 2012

summary: bra-inra09-02_bioen_nitrogen - nitrate induction - nlp mutants - Short term nitrate induction kinetics in wildtype, nlp7-1, nlp7-3 and nlp6nlp7 - 10 days old seedling grown in liquid culture on 3mM nitrate wer starvec for N for 3 days and the kinetic for the resupply of nitrate was studied during a short kinetic (0,5, 10,20 minutes).

overall_design: 26 dye-swap - gene knock out,time course

first: Anne

last: Krapp

first: Ludivine

last: Taconnat

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Discrete molecular states in the brain accompany changing responses to a vocal signal.

status: Public on Mar 15 2012

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

institute: University of Illinois

summary: New experiences can trigger changes in gene expression in the brain. To understand this phenomenon better, we studied zebra finches hearing playbacks of birdsong. Earlier research had shown that initial playbacks of a novel song transiently increase the ZENK (ZIF-268, EGR1, NGFIA, KROX-24) mRNA in the auditory forebrain, but the response selectively habituates after repetition of the stimulus. Here, using DNA microarray analysis, we show that novel song exposure induces rapid changes in thousands of RNAs, with even more RNAs decreasing than increasing. Habituation training leads to the emer- gence of a different gene expression profile a day later, accompanied by loss of essentially all of the rapid "novel" molecular responses. The novel molecular profile is characterized by increases in genes involved in transcription and RNA processing and decreases in ion channels and putative noncoding RNAs. The ‘‘habituated’’ profile is dominated by changes in genes for mitochondrial proteins. A parallel proteomic analysis [2-dimensional difference gel electrophoresis (2D-DIGE) and sequencing by mass spectrometry] also detected changes in mito- chondrial proteins, and direct enzyme assay demonstrated changes in both complexes I and IV in the habituated state. Thus a natural experience, in this case hearing the sound of birdsong, can lead to major shifts in energetics and macromolecular metabolism in higher centers in the brain.

overall_design: Adult male zebra finches were acoustically isolated and exposed to silence, novel song, or familiar song (exposure to testing song for 3 hours on the day prior to testing) on test day. The auditory lobule (AL) was collected 30 minutes after the onset of the testing experience. All samples were hybridized against the universal SoNG reference RNA pool, 6 biological replicates per group in each of 3 groups.

first: Shu

last: Dong

middle: L

first: Linda

last: Hasadsri

first: Brain

middle: S

last: Imai

first: Peter

last: Yau

first: Sandra

last: Rodriguez-Zas

first: Bruce

last: Southey

first: Jonathan

middle: V

last: Sweedler

first: David

middle: F

last: Clayton


title: Salmonella response to copper and zinc

city: Cambridge

first: Lucas

middle: Blas

last: Pontel

state: cambridgeshire

address: Francis Crick Avenue

department: PNAC

country: United Kingdom

institute: LMB-MRC

summary: Salmonella can infect a wide range of hosts and survive in the environment. This invasive pathogen has therefore evolved and acquired specific traits to cope with different, and in most cases unfavorable, conditions. In particular, transition metal ions are widely spread in these niches. These ions are essential in biology and play key roles in the structure-function of a large number of proteins. They can also be toxic, especially at high concentrations. Intracellular metal ion concentrations must therefore be tightly controlled to maintain normal metabolism. Salmonella has acquired traits to deal with the presence of toxic concentrations of some of these ions and, at the same time, to fulfill its requirement for essential metal ions when they are scarce. In this work we analyze the transcriptional response of Salmonella enterica to copper and zinc, two of these essential metals, in both rich (SLB) and defined (M9) media and at short times (10 minutes). This tiling-array based work provides a detailed description of the main transcriptional response when Salmonella detects fluctuations in copper and zinc concentrations.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: 14028s cells were grown up to OD 0.6, then, copper 10 uM (M9) or 1 mM (SLB) or Zn 50uM (M9) or 0.25 mM (SLB) was added  and bacteria were grown for 10 minutes, RNA was isolated after this time. The RNA from bacteria grown without metal was also isolated. Each sample was analized by duplicate.

middle: B

first: Michael

last: McClelland


title: Gene expression profiling in HEK293 cells overexpressed lactoferrin gene that has the signal sequence (sLF) or not (ΔLF)

status: Public on Sep 07 2011

city: seoul

first: Ju Hee

last: Kim

address: pil-dong 3-ga

department: Life Science

country: South Korea

institute: Dongguk University

summary: Human lactoferrin (LF) is a multifunctional protein involved in immunomodulation, cell growth, and differentiation. In addition to the secreted form (sLF), an alternatively spliced form (ΔLF) that lacks the signal sequence and downregulated in cancer was found. This study was carried out to identify and compare signaling networks provoked by the two LF isoforms. To do this, the two forms were overexpressed in HEK293 cells using the flp-in/tet-on system and genome-wide expression analysis of 18,367 genes was conducted.

overall_design: Secreted form (sLF) or alternatively spliced form (ΔLF) were overexpressed in HEK293 cells using the flp-in/tet-on system and genome-wide expression analysis of 18,367 genes was conducted.

first: Sun-Jung


title: Gene expression in response to the expression of the bacterial type 3 effector DspA/E

status: Public on Nov 01 2011

first: Soubigou-Taconnat

last: Ludivine

summary: au10-11_dspa - Induction of DspA/E expression in a transgenic A. thaliana line - Does DspA/E repress defenses at the transcriptionnal level? What defenses are triggered directly in response to the perception of DspA/E? - Transgenic lines expressing a GFP::DspA/E fusion or GFP alone were treated with estradiol or with DMSO. Sample were collected 6 hours following treatment.

overall_design: 8 dye-swap - gene knock out,genotype comparaison,treated vs untreated comparison

first: Mathilde

last: Fagard


title: C. elegans germline-ablated (Z2-, Z3-) animals versus intact animals, N2 strain

status: Public on Mar 01 2013

city: Ipswich

first: Amit

last: Sinha

state: MA

address: 240 County Road

institute: New England Biolabs

summary: Transcriptional profiling of C. elegans germline-ablated worms versus unablated intact animals, N2 strain

overall_design:
One-condition experiment.
C. elegans germline-ablated versus intact N2. 3 biological replicates, including 1 dye-swap.

first: Robbie

last: Rae


title: MCF7 cells gene expression change by inducing CpG demethylation using 5-Aza-2'-deoxycytidine (Aza)

status: Public on Aug 18 2011

summary: Promoter methylation is able to induce downregulation of gene expression. 5-Aza-2'-deoxycytidine(Aza), methytransferase inhibitor, induce CpG demethylation. Here, 5-Aza-2'-deoxycytidine(Aza) is treated in a human breast cancer cell, MCF7, for detection of gene expression change.

overall_design: To analyze gene expression change by aza, control RNA isolated from MCF-7 was compared with RNA isolated from MCF-7 treated with 5uM and 10uM aza.


title: Dietary exposure of 17-alpha ethinylestradiol modulates physiological endpoints and gene signaling pathways in female largemouth bass (Micropterus salmoides)

status: Public on Mar 24 2011

city: Gainesville

first: Reyna

middle: Cristina

last: Colli-Dula

state: Florida

address: Mowry Drive 471

department: CEHT

institute: University of Florida

summary: 17alpha-ethinylestradiol (EE2), used for birth control in humans, is a potent estrogen that is found in wastewater at low concentrations (ng/L). EE2 has the ability to interfere with the endocrine system of fish, affecting reproduction which can result in population level effects. The objective of this study was to determine if dietary exposure to EE2 would alter gene expression patterns and key pathways in the liver and ovary and whether these could be associated with reproductive endpoints in female largemouth bass (LMB) during egg development. Female LMB received 70 ng EE2/g feed (feed administered at 1% of body weight) for 60 days. EE2 dietary exposure significantly reduced plasma vitellogenin concentrations by 70%. Hepatosomatic and gonadosomatic indices were also decreased with EE2 feeding by 38.5% and 40%, respectively. Transcriptomic profiling revealed that there were more changes in steady-state mRNA levels in the liver compared to the ovary. Genes associated with reproduction were differentially expressed such as vitellogenin in the liver and aromatase in the gonad. In addition, a set of genes related with oxidative stress (e.g., glutathione reductase and glutathione peroxidase) were identified as altered in the liver and genes associated with the immune system (e.g., complement component 1, and macrophage-inducible C-type lectin) were altered in the gonad. In a follow-up study with 0.2 ng EE2/g feed for 60 days, similar phenotypic and gene expression changes were observed that support these findings with the higher concentrations. This study provides new insights into how dietary exposure to EE2 interferes with endocrine signaling pathways in female LMB during a critical period of reproductive oogenesis.

overall_design: Dietary exposure to EE2 would alter gene expression patterns and key pathways in the liver and ovary and these could be associated with reproductive endpoints in female largemouth bass during maturation. Female LMB received about 351 ng EE2 per day (from EE2-laced feed containing 70ng EE2/g feed) for 60 days.

middle: C

first: Christopher

middle: J

last: Martyniuk

first: Kevin

last: Kroll

first: Melinda

last: Prucha

first: Marianne

last: Kozuch

last: Barber

first: Nancy

last: Denslow


title: Common neuroinflammatory pathways in neurodegenerative diseases.

status: Public on Jan 29 2011

city: London

first: Pascal

middle: Francis

last: Durrenberger

address: hammersmith hospital, Du cane road

department: Infectious disease and immunity

institute: Imperial College London

summary: Neurodegenerative diseases of the central nervous system are characterised by pathogenetic cellular and molecular changes in specific areas of the brain that lead to the dysfunction and/or loss of explicit neuronal populations. Despite exhibiting different clinical profiles and selective neuronal loss, common features such as abnormal protein deposition, dysfunctional cellular transport, mitochondrial deficits, glutamate excitotoxicity and inflammation are observed in most, if not all, neurodegenerative disorders, suggesting converging pathways of neurodegeneration. We have generated comparative genome-wide gene expression data for Alzheimer’s disease, amyotrophic lateral sclerosis, Huntington’s disease, multiple sclerosis, Parkinson’s disease and schizophrenia using an extensive cohort of well characterised post-mortem CNS tissues. The analysis of whole genome expression patterns across these major disorders offers an outstanding opportunity not only to look into exclusive disease specific changes, but more importantly to uncover potential common molecular pathogenic mechanisms that could be targeted for therapeutic gain. Surprisingly, no dysregulated gene that passed our selection criteria was found in common across all 6 diseases using our primary method of analysis. However, 61 dysregulated genes were shared when comparing five and four diseases. Our analysis indicates firstly the involvement of common neuronal homeostatic, survival and synaptic plasticity pathways. Secondly, we report changes to immunoregulatory and immunomodulatory pathways in all diseases. Our secondary method of analysis confirmed significant up-regulation of a number of genes in diseases presenting degeneration and showed that somatostatin was downregulated in all 6 diseases. The latter is supportive of a general role for neuroinflammation in the pathogenesis and/or response to neurodegeneration. Unravelling the detailed nature of the molecular changes regulating inflammation in the CNS is key to the development of novel therapeutic approaches for these chronic conditions.

overall_design: A total of 113 cases were selected retrospectively on the basis of a confirmed clinical and neuropathological diagnosis and snap-frozen brain blocks were provided by various tissue banks within the BrainNet Europe network. Total RNA was extracted from dissected snap-frozen tissue (< 100 mg) by the individual laboratories according to a BNE optimised common protocol using the RNeasy(r) tissue lipid mini kit (Qiagen Ltd, Crawley, UK) according to the manufacturer's instructions, and was stored at -80C until further use. Gene expression analysis was performed on the RNA samples using the Illumina whole genome HumanRef8 v2 BeadChip (Illumina, London, UK). All the labelling and hybridisation of the samples was carried out in a single experiment by the Imperial College group to reduce the technical variability. RNA samples were prepared for array analysis using the Illumina TotalPrep(tm)-96 RNA Amplification Kit (Ambion/Applied Biosystems, Warrington, UK). Finally, the BeadChips we  re scanned using the Illumina BeadArray Reader. The data was extracted using BeadStudio 3.2 (Illumina). Data normalisation and gene differential expression analyses were conducted using the Rosetta error models available in the Rosetta Resolver(r) system (Rosetta Biosoftware, Seattle, Wa, USA). Two samples presented very low signal expression most likely due to hybridization problems and did not pass the quality control test. They are not represented here. One of the 2 samples was a replicate, therefore there was loss of only 1 case bringing the grand total of cases used to 112 (total of samples of 118 including 6 replicates).

first: Shama

last: Fernando

first: Samira

last: Kashefi

first: Tim

last: Bonnert

first: Isidro

last: Ferrer

first: Danielle

last: Seilhean

first: N

last: Oumesmar

first: Andrea

last: Schmitt

first: Peter

last: Gebicke-Haerter

last: Falkai

first: Edna

last: Grünblatt

first: Miklos

last: Palkovits

first: Thomas

last: Arzberger

first: Hans

last: Kretzschmar

last: Dexter

first: Richard

last: Reynolds


title: Human THP-1 Cells: Uninfected vs. Coxiella burnetii NMII infected compared to Uninfected with Chloramphenicol vs. Coxiella burnetii NMII infected with Chloramphenicol

status: Public on Oct 01 2010

city: STILLWATER

first: SAUGATA

last: MAHAPATRA

state: OK

address: 307 LSE, OSU

department: MICROBIOLOGY AND MOLECULAR GENETICS

institute: OKLAHOMA STATE UNIVERSITY

summary: A comparison was made between the THP-1(Human monocytic leukemia cells - TIB-202; ATCC) transcriptional responses of; (i) uninfected versus Coxiella burnetii NMII infected and (ii) uninfected versus Coxiella burnetii NMII infected THP-1 cells transiently treated with bacteriostatic levels (10μg/ml) of chloramphenicol (CAM). Briefly, infections were initiated and cultured in parallel with uninfected cells. At 48 hours post infection (hpi), media containing CAM (10μg/ml) was added to one set of cells (uninfected and infected THP-1 cells) and culturing was continued. The other set of cells were mock treated with normal media. Total RNA was isolated at 72 hpi from all conditions. Microarrays were performed for both condition sets and the results from each of the two microarrays were compared to define the host genes modulated by de novo C. burnetii NMII protein synthesis.

overall_design: Two-condition experiment, Human THP-1 cells: Uninfected vs. Coxiella burnetii NMII infected compared to Uninfected with Chloramphenicol vs. Coxiella burnetii NMII infected with Chloramphenicol. Biological replicates: 3, Technical replicates: 2 for both Microarrays - Uninfected vs. Coxiella burnetii NMII infected and Uninfected with Chloramphenicol vs. Coxiella burnetii NMII infected with Chloramphenicol. One Technical replicate per array. One Biological replicate per 2 arrays.

first: Saugata

last: Mahapatra

first: Patricia

last: Ayoubi

first: Edward

last: Shaw


title: Analysis of transcriptome in ectopic versus orthotopic thyroid tissue.

status: Public on Oct 28 2010

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: Congenital hypothyroidism from thyroid dysgenesis (CHTD) is a sporadic disease characterized by defects in the differentiation, migration or growth of thyroid tissue. Of these defects, incomplete migration resulting in ectopic thyroid tissue is the most common (up to 80%). We obtained flashfrozen samples of ectopic thyroid tissue removed from 3 girls aged 8, 10 and 15 yr, because it caused local symptoms. For comparison, we used orthotopic thyroid tissue from a Caucasian female, age 68 with gall bladder cancer. Analysis of transcriptome revealed up to 1011 genes more than twofold induced or repressed.

overall_design: Microarray hybridization was performed on three independent pairs of ectopic thyroids (one pair performed in duplicate) compared to control thyroid tissue. After amplification and labelling, sample pairs were hybridized onto Human Exonic Evidence Based Oligonucleotide HEEBO slides (Stanford Functional Genomics Facility, CA). The oligonucleotide set consists of 44544 70-mer probes that were designed using a transcriptome-based annotation of exonic structure for genomic loci. Hybridizations were replicated with dye swap.

first: Rasha

last: Abu-Khudir

first: Jean

last: Paquette

first: Anne

last: Lefort

first: Jean-Pierre

last: Chanoine

first: Gilbert

last: Vassart

first: Guy

last: Van Vliet

first: Johnny

last: Deladoëy


title: Gene expression analysis of gamma-M.tuberculosis-stimulated CD14hiCD16- and CD14loCD16+ monocytes

status: Public on Nov 23 2010

city: Tyler

first: Rohan

last: Dhiman

state: Texas

department: Centre for Pulmonary and Infectious Disease Control

institute: University of Texas Health Science Center at Tyler

summary: Current study will help us to elucidate the differential gene expression profiles of two different subsets of monocytes stimulated with gamma-M. tuberculosis

overall_design:
CD14hiCD16- and CD14loCD16+ monocytes were isolated from human peripheral blood using magnetic beads for CD14 and CD16. 1.5 million cells were cultured in 1 ml of complete RPMI medium and stimulated with 10 microgram/ml of gamma-M. tuberculosis for 48 hours. After 48 hours cells were harvested and RNA was isolated from control and stimulated samples from CD14hiCD16- and CD14loCD16+ monocytes. So total we had 4 samples: 1. Control CD14hiCD16- 2. Stimulated CD14hiCD16- 3. Control CD14loCD16+ monocytes and 4. CD14loCD16+ monocytes.
RNA from all these above 4 samples were sent to Phalanx Biotech Group for whole genome microarray.

first: Anuradha

last: Bandaru

first: Peter

last: Barnes

first: Sudipto

last: Saha

first: Amy

last: Twinnereim

first: Ramesh

last: Nayak

first: Padmaja

last: Paidipally

first: Vijayalaxmi

last: Valluri

first: Vijaya

middle: M

last: Rao

first: Ramakrishna

last: Vankayalapati


title: The gene profile analysis of the function of HMGA2 in immortalized human ovarian surface epithelial cell lines.

status: Public on Aug 14 2010

city: Chicago

first: Jingjing

last: Wu

address: 303 E. Chicago Avenue

department: pathology

institute: northwestern university

summary: To identify HMGA2-regulated downstream target genes, we compared the difference of gene profiles between ovarian surface epithelial cells without HMGA2 (T29-1, T29-2, T80) and cells with HMGA2 (T29A2-8, T29A2-15, T80A2-11).

overall_design: Immortalized ovarian surface epithelial cells (named T29-1, T29-2, T80) were transfected with HMGA2 retrovirus vector pBabe-HMGA2 (named T29A2-8, T29A2-15, T80A2-11). Then cells were harvested for RNA isolation for gene expression analysis. Control group: T29-1, T29-2, T80. Testing group: T29A2-8, T29A2-15, T80A2-11.

first: Jianjun

last: Wei


title: Whole Genome Expression in Peripheral-Blood Samples of Workers Professionally Exposed to Polycyclic Aromatic Hydrocarbons

status: Public on Sep 21 2011

city: Kaohsiung

first: Tzu Chi

last: Lee

address: Shihcyuan 1st Rd.

department: Department of Public Health

institute: Kaohsiung Medical University

summary: This study aims to examine global gene expression profiles before and after the work-shift among coke-oven workers (COW). COW work six consecutive days and then take two days off. Two blood and urine samples in each worker were collected before starting to work after two-days off and end-of-shift in the sixth-day work in 2009. Altered gene expressions (ratio of gene expression levels between end-of-shift and pre-shift work) were performed by Human OneArray expression system which probes ~30,000-transcription expression profiling of human genes. Sixteen workers, all men, were enrolled in this study. Median urinary 1-hydroxypyrene (1OHP) levels (umole/mole creatinine) in end-of-shift work were significantly higher than those in pre-shift work (2.58 vs. 0.29, p = 0.0002). Among the 20,341 genes which passed experimental quality control, 26 gene expression changes, 7 positively- and 19 negatively-, were highly correlated with across-the-shift urinary 1OHP levels (end-of-shift – pre-shift 1OHP) (p-value < 0.001). The high and low exposure groups of across-the-shift urinary 1OHP levels dichotomized in ~2.00 µmole/mole creatinine were able to be distinguished by these 26 genes. Some of them are known to be involved in apoptosis, chromosome stability/DNA repair, cell cycle control/tumor suppressor, cell adhesion, development/spermatogenesis, immune function, and neuronal cell function.

overall_design: Sixteen coke-oven workers who had worked in one of two coke-oven plants for at least one year in the largest steel company in Taiwan voluntarily participated in this study between July-October, 2009. Coke-oven workers regularly work 6 days and take two days off. Thus, we collected their blood and urine samples at two different time points: one was during the pre-shift work on the first day after two days off, and the second one was at the end-of-shift work on the 6th work day.  Information about age and smoking status was also collected before the collection of biological specimens.

first: Ming-Tsang

first: Chih-Hong

last: Pan

first: Hung-Ju

last: Su

first: Jie-Len

last: Huang

first: Chiung-Yu

last: Peng

first: Weihsin

last: Wang

first: Ting-Yu

last: Chou

first: Ming-Yen

last: Lin

first: Wen-Yi

first: Chia-Tsuan

first: Tzu-Chi

first: Chi-Kung

last: Ho


title: mutant vs wildtype-Embryonic patterning in Arabidopsis thaliana

status: Public on May 01 2010

city: evry

first: Soubigou-Taconnat

last: Ludivine

institute: INRA

summary:
adt05-04_drn - mutant vs wildtype - DRN targets  - Ovules containing heart-stage/torpedo-stage embryos were dissected from siliques and imidiately shock frozen in liquid nitrogen. RNA was extracted and sent to Evry for comparison between mutant and wildtype transcriptome.

Keywords: gene knock out

overall_design: 2 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Wolfgang-

last: Werr

first: Marie-Laure

last: Martin-Magniette


title: uprt overexpression - Transcriptomic analysis of overexpression of the URPT gene

status: Public on Feb 01 2011

summary: adt10-02_35suprt - uprt overexpression. Transcriptomic analysis of the overexpression of UPTR.

overall_design: 8 dye-swaps. Normal vs. transgenic comparison.

first: Sandrine

last: Balzergue


title: Microarray analysis of aristolochic acid in normal human cells

status: Public on Sep 24 2010

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

institute: China Medical University

summary: Aim： Use microarray analysis to understand the molecular mechanism underlying the effect of aristolochic acid (AA), a major active component of plants from the Aristolochiaceae family, in normal human kidney (HK-2) cells. Methods： HK-2 cells were treated with AA  for 24 hours and cell viability was measured by a 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazolium bromide assay. Complementary DNA microarrays were used to investigate the gene expression pattern of HK-2 cells exposed to AA and the results of this study were in triplicate. Quantitative real-time RT-PCR assay was used to verify the microarray data for selected nuclear factor kappa B (NF-κB)-regulated genes. Furthermore, subcellular localization of NF-κB p65 was visualized by immunofluorescence confocal microscopy in HK-2 cells. NF-κB activity was examined by luciferase reporter assay in HK-2/NF-κB transgenic cells. Results： AA exhibited a dose-dependent cytotoxic effect in HK-2 cells and induced alterations in gene expression profiles related to DNA damage response, stress response, etc. In addition, 9 biological pathways associated with immunomodulatory functions were down-regulated in AA-treated HK-2 cells. Network analysis revealed that NF-κB played a central role in the network topology. Among NF-kB-regulated genes, 8 differentially expressed genes were verified by real-time RT-PCR. The inhibition of NF-κB activity by AA was further confirmed by immunofluorescence confocal microscopy and by NF-κB luciferase reporter assay. Conclusion： Our data revealed that AA could suppress NF-κB activity in normal human cells, perhaps partially accounting for the reported anti-inflammatory effects of some plants from the genus Aristolochia.

overall_design: HK-2 cells were grown in keratinocyte serum-free basal medium (Gibco) supplemented with 5 ng/ml of recombinant epidermal growth factor and 50 μg/ml of bovine pituitary extract without antibiotics in 5 % CO2 at 370C. HK-2 cells were seeded in 25-T flasks and incubated for 24 h before aristolochic acid treatment. Aristolochic acid (10 90 μM) were added to HK-2 cells for 24 h. The control cells received equal amounts of water only.

first: Ya-Yin

last: Chen

first: Su-Yin

last: CHIANG

first: Hsu-Ching

last: WU

first: Shung-Te

last: KAO

last: HSIANG

first: Tin-Yun

last: HO

first: Jaung-Geng

last: LIN


title: Transcription profiling of Caco-2 cells and Clostridium difficile during infection

status: Public on Aug 07 2010

city: Ithaca

first: Tavan

last: Janvilisri

state: NY

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

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

summary: Clostridium difficile is an anaerobic spore-forming rod-shaped gram-positive bacterium that can infect both humans and animals. Most studies on the pathogenesis of C. difficile have focused on its toxins and their effect on the host cells. Recently, we utilized microarrays to identify conserved and divergent genes associated with virulence in C. difficile isolates from humans and animals. Our data provided the first clue toward a complex mechanism underlying host adaptation and pathogenesis. Microarray technology offers an efficient high-throughput tool to study the transcriptional profiles of pathogens and infected host cells. Transcriptomes of C. difficile after exposure to environmental and antibiotic stresses and those of human epithelial colorectal Caco-2 cells upon TcdA treatment have been analyzed. To our knowledge, there are still no reports on the transcriptomic study of host-pathogen interactions for C. difficile infection (CDI). In vitro analyses of interplay between host and pathogen are essential to unravel the mechanisms of infection and to investigate the host response to infection. We therefore employed microarrays to study both bacterial and human cellular transcriptome kinetics during CDI to Caco-2 cells. Here we present a large-scale analysis of transcriptional profiles to reveal molecular determinants playing a role in C. difficile pathogenesis and the host response. We found that there were 254 and 224 differentially-expressed genes after CDI in C. difficile and Caco-2 cells, respectively. These genes are clustered according to their functional categories and their potential roles in pathogenesis and host response are discussed. Our results will not only increase our understanding on the host-pathogen interaction, but may also provide targets for drug development.

sample_organism:
Clostridioides difficile
Homo sapiens
Clostridioides difficile 630

platform_organism:
Clostridioides difficile
Homo sapiens

overall_design:
Clostridium difficile: Control vs Infection (time course)
mRNA with genomic DNA of tested and reference strains

Caco-2 cells: Control vs Infected with Clostridium difficile
Time-course experiments of Caco-2 cells infected with C. difficile for 30, 60 and 120 min

first: Yung-Fu

last: Chang

first: Joy

last: Scaria


title: defenses mechanism in response to cold stress-PI4kinases and Long-chain bases kinases in response to cold stress

status: Public on Mar 23 2012

last: Ludivine

summary: au10-10_froid - defenses mechanism in response to cold stress - Role of PI4 kinase and Long-chain bases kinases in response to cold stress - Plantlets of wild type and mutant were grown vitro for 14 days in a growth chamber (80% humidity, 80 micro Enstein without photoperiod). The 15th day, plantlets were transferred at 4°C or 12°C during 4 hours (80 micro Enstein) for the cold stress.

overall_design: 14 dye-swap - treated vs untreated comparison

first: Delphine

last: Gey

first: Juliette

last: Puyaubert


title: The mental retardation gene PHF8 mediates histone H4K20/H3K9 demethylation and regulates zebrafish brain apoptosis and craniofacial development: expression analysis

status: Public on Jul 14 2010

city: Boston

first: Hank

middle: heng

last: qi

address: NRB 854, 77 Ave. Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: PHF8 (PHD Finger 8) mutations have been found in patients with X-linked mental retardation (XLMR) and craniofacial deformities. Here we identify PHF8 as the first enzyme that mediates demethylation of mono-methylated histone H4 lysine (K) 20 (H4K20me1), with additional activities towards H3K9me2/1 and H3K27me2. Patient mutations significantly compromise the demethylase activity, indicating functional importance. ChIP-seq identified PHF8 near the transcription start sites (TSS) of over 7000 target genes as well as in gene bodies and intergenic regions. PHF8 depletion resulted in up-regulation of H4K20me1 and H3K9me1 at the TSS-associated sites, and H3K9me2 in the gene bodies and intergenic regions, respectively, demonstrating differential substrate specificities at different target genomic locations. PHF8 depletion at the TSS results in decreased target gene expression, which is coincident with increased occupancy of the protein L3MBTL1 previously shown to induce chromatin compaction via binding to lower methyl states including H4K20me1 and H3K9me1.

overall_design: PHF8 RNAi and control RNAi stable HeLa cell lines were established. RNA were isolated from triplicate cell cultures. RNAs were subject to microarray expression analysis. Hybridizations were performed in duplicate.

middle: H

last: Qi

first: Yang

last: Shi


title: Exogenous expression of CC3/TIP30 in U373 cells with or without UV treatment

status: Public on Mar 05 2010

city: Emeryville

first: Sylvia

last: Fong

address: 5858 Horton St Suite 400

institute: Bionovo Inc

summary: The pro-apoptotic protein CC3/TIP30 has an unusual cellular function as an inhibitor of nucleocytoplasmic transport. This function is likely to be activated under conditions of stress. Here we examined the potential role of CC3 in regulation of cellular responses to genotoxic stress. We found that forced expression of CC3 in CC3-negative cells delays repair of both UV-induced and oxidative DNA damage. Exogenously introduced CC3 negatively affects expression levels of DDB2 and p21CIP11 and inhibits induction of c-FOS after UV exposure, which is likely to contribute to the observed delay in DNA damage repair. The increase in nuclear localization of p21CIP11 observed after UV exposure is diminished in cells expressing exogenous CC3. Expression of CC3 also delays repair of oxidative DNA damage and leads to a decrease in levels of nucleoredoxin. Silencing of CC3 in CC3-positive cells has a modest delaying effect on repair of the UV induced damage, but has a much more significant negative affect on the translesion DNA synthesis after UV exposure. This could be related to the higher expression levels and increased nuclear localization of p21CIP11 in cells where expression of CC3 is silenced.  Apparently, manipulation of the cellular levels of CC3 adversely affects DNA damage responses by affecting the levels and subcellular localization of relevant proteins.

overall_design: 4 groups - U373 Neo Control, U373 CC3, U373 Neo Control UV, U373 CC3 UV. Each group has 3 biological replicates. Each biological replicates has 3 technical replicates.

first: Emma

last: Shtivelman


title: Gene expression profiling in p53 and p73 double knockdown HCT116-3(6) cells

status: Public on Jun 30 2009

city: La Jolla

first: Vera

last: Huang

address: 3855 Health Science Drive, Room 4317

department: Medicine

institute: UCSD-Moores Cancer Center

summary: The main goal of this study is to integrate gene expression analysis with ChIP-chip study.  To examine the relationship between promoter occupancy and gene expression, we transiently depleted p53 and p73 via small interfering RNA (siRNA) in HCT116-3(6) cells and then performed microarray analysis of 32,000 genes before or after HU treatment using the Phalanx expression array platform. We found that only 6%-14% of p53 and p73 bound promoters at FDRMAP <0.05 exhibited significant changes in mRNA expression when p53 and p73 were simultaneously knocked-down by siRNA. The minimal correlation between binding and regulation of expression is consistent with previous observations of the lack of transcriptional effects at many transcription factor binding sites.

overall_design: HCT116-3(6) cells were transiently transfected with lacZ siRNA or p53/p73 siRNA oligo and were then treated with or without HU for 16 hrs. Four biological repeats were performed for each condition (-HU or +HU), with two technical repeats (dye swap) per biological sample.

first: Xin

last: Lu

first: Yong

last: Jiang

first: Jean

middle: Y

last: Wang


title: Expression Profiling of Androgen Receptor and Vitamin D Receptor Mediated Signaling in Prostate Cancer Cells

status: Public on Jul 31 2009

city: Rensselaer

first: Sridar

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Studies of gene expression profiles using the whole genomewide microarray analysis in LNCaP cells (AR+, p53wt) when treated with 5nM testosterone and 100nM 1,25(OH)2D3 alone or in combination. Comparisons between each treatment groups provide evidence for the crosstalk between VDR and AR mediated signaling events at the transcriptional levels, which may have significant clinical impact in patient care.

overall_design: Three independent experiments were carried out in LNCaP cells, which were treated with ethanol control (no exogenous androgen), 5nM testosterone, 100nM 1,25(OH)2D3, and the combination of testosterone and 1,25(OH)2D3. Total RNA was extracted from cell lysates using QIAGEN midiRNeasy kit after 48h of treatment. The samples were run on 12 chips such that each chip measures the expression levels of 24,000 genes from Homo sapiens with 60-mer probe pairs, with three-fold redundancy.

first: Martin

last: Tenniswood

first: Wei-Lin


title: Gene Expression in Cisplatin Resistance HeLa Cells

city: Kwei-San

first: Ching-Kuey

middle: Chuck

last: Chao

state: Tao-Yuan

address: 259, Wen-Hwa 1 Rd

department: Biochemistry and Molecular Biology

institute: Chang-Gung University

summary: Cisplatin resistance is a problem in cancer treatment. Using DNA microarray, we detected differentially expressed genes in cisplatin-resistant cervix carcinoma HeLa cells compared to parental cells.

overall_design: Three cisplatin resistant cell lines were established by stepwise increasing cisplatin concentration. RNA from these resistant lines and its parental HeLa cells were labeled with Cy5 and Cy3. Equal amount of RNA from resistant cell line and HeLa were mixed and were hybridized to cDNA array. Signals were scanned and analyzed to find out the candidate genes involved in cisplatin resistant mechanism.

first: Hsing-Pang

first: C


title: Cell cycle and cell death interaction in plants: PCNA, AtXRs and AtMIPS pathway.

status: Public on Mar 07 2009

first: Soubigou-Taconnat

address: 2 rue gaston crémieux

summary:
rs07-04_mips - atmips mutant/photoperiod - In Arabidopsis thaliana, how does MIPS knock out influence gene expression? In AtMIPS mutants how does photoperiod influence gene expression. - Wild type Colombia and MIPS mutant (Salk 023626) plants are grown in short days (8h light) during 27 days and then transfered in long days (16h light) during 4 days. J4JC correspond to 27+4=31 days plants in short days.

Keywords: gene knock out

overall_design: 6 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

middle: P

last: Renou

first: Catherine-

last: Bergounioux

first: Marie-Laure

last: Martin-Magniette


title: treatment g-butyrobetaine wt col.0-Effect of carnitine on the transcriptome of A. thaliana

status: Public on Feb 18 2009

city: Evry Cedex

first: Agnes

last: Yu

address: 2 rue Gaston Cremieux CP 5708

summary:
rs07-01_carnitine - treatment g-butyrobetaine wt col.0 - Effect of carnitine on the transcriptome of A. thaliana - Seedlings WT are growing in a independent way on media MS. After seven days of culture, seedling are harvested and a pull is formed from the three prelevements. Extractions of RNA will be realised on this pull. We proceed in a identical way for the test sample. Seedlings are cultivated on media MS containing butyrobétaïne 1 mM. After seven days, seedlings are harvested and extractions of RNA will be realised on this second pull. All this experiment is repeated one more time independently.
Keywords: treated vs untreated comparison

first: Yolande

last: Perrin


title: The global responses of human bone marrow-derived mesenchymal stem cells to baculovirus transduction

status: Public on Apr 30 2009

city: Hsinchu

first: Yu-Chen

last: Hu

address: 101, Section 2, Kuang-Fu Road

department: Chemical Engineering

institute: National Tsing Hua University

summary: Human mesenchymal stem cells (hMSCs) are a promising cell source for regenerative medicine and can be genetically modified with viral vectors, yet how hMSCs respond to viral vector transduction remains poorly understood, leaving the safety concerns unaddressed. Hereby we explored the responses of hMSCs against an emerging DNA viral vector, baculovirus (BV), and uncovered that BV transduction perturbed the transcription of 816 known genes associated with several signaling pathways.

overall_design: Both experimental group (e.g. BV-transduced hMSCs) and control group (e.g. mock-transduced hMSCs) have four replicates respectively.

first: Guan-Yu

last: Chen

first: Hsiao-Chiao

last: Shiah

first: Hung-Ju

last: Su

first: Chi-Yuan

first: Yung-Jen

last: Chuang

first: Wen-Hsin

last: Lo

first: Jie-Len

first: Ching-Kuang

first: Shiaw-Min

last: Hwang


title: Two Supporting Factors Greatly Improve the Efficiency of Human iPS Cell Generation

status: Public on Nov 07 2008

city: Beijing

first: hongkui

last: deng

address: Yiheyuan Road 5#, Haidian District

department: College of Life Sciences

institute: Peking University

summary:
Human fibroblasts can be induced into pluripotent stem cells (iPS cells), but the reprogramming efficiency is quite low. Here, we screened a panel of candidate factors in the presence of OCT4, SOX2, KLF4 and c-MYC in an effort to improve the reprogramming efficiency from human adult fibroblasts. We found that p53 siRNA and UTF1 enhanced the efficiency of iPS cell generation up to 100-fold, even when the oncogene c-MYC was removed from the combinations. We further demonstrated that by using a novel combination of the four factors OCT4, SOX2, KLF4 and UTF1, iPS cells could be generated at a frequency at least 10 times higher than using the original four reprogramming factors without c-MYC. The iPS cells generated in this work have a similar gene expression profile and differentiation potential as human embryonic stem (hES) cells. In conclusion, two novel supporting factors that increase the efficiency of direct reprogramming have been identified, and a more-efficient method for the generation of human iPS cells has been developed in the absence of the oncogene c-MYC.

Keywords: cell type comparison

overall_design: Total RNA from hFSF, hAFF, hES cells (H1, H7) and 7 established iPS cell lines were labeled with Cy5, hybridized to a human Oligo Microarray (Phalanx Human Whole Genome OneArray™, Phalanx Biotech) according to the manufacturer's protocol. Three technical repetitions were performed. After hybridization, arrays were scanned using GenePix 4000B scanner (Molecular Devices) and processed using the GenePix Pro 6.0 software (Molecular Devices). After removing control probes, a 14/33 presence call (SNR>=5 and foreground-background>0) was used to filter probes for the 33 microarrays, resulting in 12311 probes for further quantile normalization.

first: Yang

last: Zhao

first: Xiaolei

last: Yin

first: Han

last: Qin

first: Hongkui

last: Deng


title: drn/drn-l expressing cells vs non-expressing cells-Embryonic patterning in Arabidopsis thaliana

first: Soubigou-Taconnat

last: Ludivine

department: URGV

summary:
adt05-04_drn - drn/drn-l expressing cells vs non-expressing cells - DRN targets - In primordia timing (pt) mutant background DRN::erGFP transgenic cell culture (somatic embryos suitable to regenerate plants) has been protoplasted and protoplasts have been sorted for GFP+ and GFP- cells. Total RNA was extracted and sent to Evry for comparison (samples DRN a,b,c). DRN-L::erGFP transgenic cell culture has been protoplasted and protoplasts have been sorted for GFP+ and GFP- cells (samples DRN-L-2-1 and DRN-L-3-1).

Keywords: null

overall_design: 5 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Wolfgang-

last: Werr

first: Marie-Laure


title: esr1-drn-Transcriptomic study of the transcription factor ESR1/DRN.

status: Public on Sep 26 2008

summary:
adt06-01_esr1-drn_dexamethasone - esr1-drn - Identification of the target genes of the ESR1/DRN TF using dexamethasone induction - Identification of the target genes of the ESR1/DRN TF using dexamethasone induction

Keywords: normal vs transgenic comparison

last: Martin-Magniette


title: flg22 time course-Gene profiling upon biotic stress treatment: Gene profiling in microRNA mutants

status: Public on Jun 02 2008

summary:
rs06-06_mirna - flg22 time course - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - 14-day old seedlings (Col-0 and fls2 KO) treated with 10uM of flg22 (flagellin derived peptide) over a one hour timecourse.
Keywords: time course,treated vs untreated comparison

overall_design: 7 dye-swap - CATMA arrays

first: Lionel

last: Navarro


title: comparison between constitutive and inducible p25 plants-Global transcriptome deregulation of P25 expressing plants

status: Public on Jan 16 2010

summary:
au08-05_p25ind - comparison between constitutive and inducible p25 plants - Are there some genes deregulated by the p25 viral protein. - Comparison between constitutive and inducible p25 plants.

Keywords: gene knock in (transgenic)

overall_design: 10 dye-swap - CATMA arrays

first: David

last: Gilmer


title: Conduritol B Epoxide treatment of MSCs and 293T cells

status: Public on Dec 15 2008

city: Houston

first: Philippe

last: Campeau

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The purpose of this study was to study the biological consequences of inhibiting acid beta-galactosidase with the use of conduritol b epoxide, which serves as a chemical model of Gaucher disease

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cells (human and murine bone marrow mesenchymal stromal cells, and 293T cells) were treated or not with Conduritol B epoxide at 100 micromolar for 5 days, before RNA was extracted and hybridized.

first: Jacques

last: Galipeau


title: Transcriptomic of meiocytes.

status: Public on Dec 07 2008

summary:
What are the gene expressed during meiosis pathway in Arabidopsis thalina. Comparison of total RNAs from isolated meiocytes with those isolated from root tips, and those from leaves. Comparison of transcriptomes of normal stamen (ecotype columbia) with root tips and leaves. And, comparison of transcriptomes of normal stamens (ecotype L. erecta) with stamens from sporocyteless mutant (L. erecta).
Keywords: organ comparison

overall_design: 11 dye-swap - CATMA arrays

first: Christine

last: Horlow


title: comparisons wt-mutants 2 -Gene profiling upon biotic stress treatment. Gene profiling in microRNA mutants.

summary:
rs06-06_mirna - comparisons wt-mutants 2  - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - Ler, dcl1-9, hen1-1 and hasty were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium and harvested 2 days after.
Keywords: gene knock out

overall_design: 3 dye-swap - CATMA arrays


title: comparisons wt-mutants 1 et 3-Gene profiling upon biotic stress treatment. Gene profiling in microRNA mutants.

summary:
rs06-06_mirna - comparisons wt-mutants 1 et 3 - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - Col-0, dcl2-1, dcl3-1 and rdr2-1 were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium and harvested 2 days after.
Keywords: gene knock out


title: flagellin experiment in dcl2-dcl3-dcl4 mutant background-Gene profiling upon biotic stress treatment.

summary:
rs06-06_mirna - flagellin experiment in dcl2-dcl3-dcl4 mutant background - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - What are the genes (including primary miRNA transcripts) that are differentially regulated upon flg22 treatment? 14-day old seedlings (Col-0 and dcl2-dcl3-dcl4) treated with flg22 (flagellin- derived peptide).
Keywords: treated vs untreated comparison

overall_design: 8 dye-swap - CATMA arrays


title: meiocytes-Transcriptomic of meiocytes.

summary:
ra05-04_meiocytes - meiocytes - What are the gene expressed during meiosis pathway in Arabidopsis thalina. - Comparison of meiocyte transcriptome versus leaf transcriptome.

Keywords: total transcriptome knowledge

overall_design: 1 dye-swap - CATMA arrays


title: flg22 treatment & mutants 2-Gene profiling upon biotic stress treatment. Gene profiling in microRNA mutants.

summary:
rs06-06_mirna - flg22 treatment & mutants 2 - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - Col-0, dcl4-1, rdr6-1 were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium 2 days after and treated with 10uM flagellin active or inactive. Samples were harvested at 30 min after treatment.
Keywords: treated vs untreated comparison


title: comparisons wt-mutants 1-Gene profiling upon biotic stress treatment. Gene profiling in microRNA mutants.

summary:
rs06-06_mirna - comparisons wt-mutants 1 - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - What are the genes (including miRNA precursors) that are differentially regulated in a set of tasiRNA mutants? Col-0, dcl4-1, rdr6-1 were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium and harvested 2 days after.
Keywords: gene knock out

overall_design: 2 dye-swap - CATMA arrays


title: agrobacterium treatment-Gene profiling upon biotic stress treatment. Gene profiling in microRNA mutants.

summary:
rs06-06_mirna - agrobacterium treatment - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - Col-0 plants were infected with wt Agrobacterium tumefaciens (strain A208) by stabbing the emerging stems. 18 days later, growing tumors were harvested as were the non-infected part of the stabbed-stem.In parallel, Col-0 seeds were germinated on Callus Induction Media (CIM) and 18 days later, calli were harvested.
Keywords: normal vs disease comparison,organ comparison


title: A Time Course Analysis of the Effects of Marinobufagenin in Human Dermal Fibroblasts

status: Public on Dec 07 2007

city: Toledo

first: Khew-Voon

last: Chin

state: OH

address: 3000 Arlington Avenue

institute: The University of Toledo College of Medicine

summary:
Gene expression profiling of the effets of marinobufagenin in a time-course study (0, 0.25, 0.5, 0.75, 1, 2, 3, 6, 9, 12, 15, and 24 hrs) to examine the temporal changes in gene expression in a human dermal fibroblast cell line.
Keywords: Time course

overall_design: Cells were treated with 10 nM of marinobufagenin (MBG) for the following times: 0, 0.25, 0.5, 0.75, 1, 2, 3, 6, 9, 12, 15, and 24 hrs, and then cells were harvested for RNA isolation for gene expression analysis.

first: Joseph

last: Shapiro


title: n509-9-Transcriptomic analyses of the N509.9 nodulin-like knock out mutant

status: Public on Mar 12 2008

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

summary:
rs06-04_noduline-like - n509-9 - What are the consequences of knocking out a nodulin-like gene? - N509.9 mutant vs wild type in 2 different stages, with biological repetition
Keywords: gene knock out,organ comparison

overall_design: 4 dye-swap - CATMA arrays

first: Deborah

last: Goffner


title: carnitine effect-Effect of carnitine on the transcriptome of A. thaliana

status: Public on Mar 05 2008

first: Agnes

last: Yu

summary:
rs07-01_carnitine - carnitine effect - Effect of carnitine on the transcriptome of A. thaliana - Our objective is the description of the existence of an intracellular transport depend on the carnitine at Arabidopsis thaliana. For that, we planned the study of the response of the transcriptome in the presence of exogenic L-carnitine. Seedlings WT are cultivated on medium MS, 6 independent times. At 144h, the seedlings are collected and pools are formed with 3 samples. We proceed in the same way for the seedlings which are cultivated on medium MS containing L-carnitine 5mM.
Keywords: treated vs untreated comparison

first: Yolande

last: Perrin


title: TGFbeta signalling in fibroblasts.

status: Public on Mar 16 2005

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

summary:
Murine embryonic fibroblasts, wild type or Alk5 knock outs, stimulated and unstimulated with TGFbeta.
Keywords: parallel sample

first: Göran

last: Karlsson

first: Yingchun

last: Liu

first: Marie-Jose

last: Goumans

first: Jonas

last: Larsson

first: Ju-Seog

last: Lee

first: Snorri

last: Thorgeirsson

first: Stefan


title: ALCAR supplementation to unloaded soleus muscle

status: Public on Jun 07 2006

city: Bari

first: Maria Nicola

last: Gadaleta

address: via Orabona 4

department: Department of Biochemistry and Molecular Biology

institute: University of Bari, Italy

summary:
The effect of acetyl-L-carnitine (ALCAR) supplementation to hindlimb suspended rats has been analyzed in order to test whether this would promote the differentiation towards an oxidative phenotype of muscle fibers in soleus muscle and prevent the transformation of this slow tonic muscle towards a glycolytic, low-oxidative phenotype due to unloading condition. 3 month-old rats were daily supplemented with ALCAR concomitantly with hindlimb suspension. Validated microarray analysis for a broad range of muscle-relevant processes delineated an ALCAR-induced adjustment of the expression profile. In particular, transcript elevations of factors underlying oxidative metabolism in mitochondria and protein turnover by ribosomal and proteasomal components as well as an adaptation of voltage-gated ion channel expression were identified as an ALCAR response in soleus muscle.
Keywords: ALCAR effect

overall_design:
21 samples total, 7 each of:
14 days age control
14-day hindlimb suspended rats
14 day hindlimb suspended rats treated with ALCAR

first: Pierluigi

last: Cassano

first: Martin

last: Fluck

first: Anna

middle: G

last: Sciancalepore

first: Vito

last: Pesce

first: Hans

last: Hoppeler

first: Palmiro

last: Cantatore

first: Maria

middle: N


title: Transcriptome response to the deletion of Gcr1, Nup84 or Nup84 & Gcr1 (double deletion)

status: Public on Aug 22 2007

city: Hattiesburg

first: Kellie

last: Barbara

state: MS

address: 118 College Dr. #5018

department: Biological Sciences

institute: Univ. of Southern MS

summary:
This experiment compares the transcriptional response of yeast cells to the deletion of Gcr1, Nup84, or both, to isogenic wild type strains grown in YPD at 23C.  The goal was to identify misregulated target genes and analyze the functional classifications of those targets.
Keywords: cell type comparison (knock-outs)

overall_design: This experiment included biological replicates as well as technical dye-swap replicates of each biological sample.

middle: E