title: Gene expression profiling of mammary epithelial cells and their role in the predisposition to Staphylococcus aureus infections

status: Public on Mar 01 2012

summary: Background: Staphylococcus aureus is a major pathogen of humans and animals. Host genetics influence the susceptibility to S. aureus infections, and genes determining infection outcome remain to be identified. Here, we used outbred animals from a divergent selection on susceptibility towards Staphylococcus infection to explore host immunogenetics. Methodology/Principal Findings: We investigated in vitro how mammary epithelial cells (MEC) respond to live S. aureus or S. aureus supernatant and whether MEC from animals with different degree of susceptibility to intra-mammary infections have distinct gene expression profiles. We measured the expression of 15K probes in MEC after each kind of stimulation (living bacteria or culture supernatant) at three different time points (a reference without bacteria, 1 and 5 hours) with ovine Agilent microarrays. Furthermore, a selected number of genes were confirmed by RT-qPCR. Gene signatures of stimulated MEC were obtained and genes involved in the cell cycle and metabolic processes were down-regulated during the kinetics and the apoptosis pathways were highly modified after both live bacteria and supernatant stimulations. Genes involved in immune response were up-regulated over-all after supernatant exposure. Furthermore 23 genes were differentially expressed between the resistant and susceptible animals, two of them were involed in oxidative processes, but the differences between the animals were very few.  Conclusion/Significance: we successfully obtained Staphylococcus aureus associated gene expression of ovine MEC in a 5 hour kinetics experiment. The in vitro MEC model does not provide much information on the differences between Staphylococcus resistant and susceptible animals. Keywords: Staphylococcus aureus ; mammary epithelial cells ; mammalian ; transcriptome ; immunity ; mastitis

overall_design: 59 samples in a two-colour dye-swap experimental design.

first: P

last: Rainard

first: F

last: Gilbert

last: Cunha

last: Robert-Granie


title: Gene expression profiling of dendritic cells derived from bone marrow (BM-DC) in response to myxoma virus infection.

status: Public on Oct 15 2011

city: Toulouse cedex 03

first: Gilles

last: FOUCRAS

address: 23, chemin des Capelles

country: France

institute: INRA

summary: Background : Poxviruses have been shown to be efficient vectors for the production of protective immune responses in host species but also in on host species. Myxoma virus belongs to poxviridae family. In order to evaluate the capacity of (MYXV)  as a vaccine vector in ruminants, we invistigated its interactions with bone marrow-derived  dendritic cells (BM-DC). DCs  are the most potent antigen-presenting cells and play a crucial role during the priming and reactivation of antigen-specific immune responses . Following infection by a pathogen, the functional changes of DC are essential since priming and polarization of the immune response depend on these changes . Therefore a better understanding of the modifications in gene expression of proinflammatory cytokines, chemokines and stimulatory molecules expression may prove useful in predicting whether or not a vaccine vector will be effective. Moreover, it may help identifying modifications for improving its efficacy.  Methodology/Principal Findings: We investigated in vitro the interactions between recombinant MYXV expressing GFP protein, SG33-GFP and ovine BM-DCs. To gain a global view of the gene remodelling induced by MYXV, we infected BM-DCs from three sheep with  SG33-GFP at different multiplicity of infection (MOI) (0, 1, 3) during different time (0, 3, 8 hours).  We measured the expression of 15K probes in BM-DCs after each kind of conditions with ovine Agilent microarrays. Furthermore, a selected number of genes were confirmed by RT-qPCR. MYXV infection induces a strong reprogramming of the cells leading to the expression of pro-inflammatory cytokines and mobilisation of type I IFN pathways, cellular death and features associated with the activation of the adaptive immune response.  Conclusion/Significance:  Microarray profiling of a poxvirus-DC interaction help to delineate some interesting features of a vector candidate in ovine, and pave the way for additional improvements of a promising platform. Keywords : Myxoma virus ; bone marrow-derived dendritic cells ; transcriptome ; sheep; vaccine

overall_design: 9 samples: 3 time points and 3 replicates of MOI=1

first: S

last: Top

first: E

last: Foulon

first: B

last: Pignolet

first: M

last: Deplanche

first: C

last: Caubet

last: Tasca

last: Bertagnoli

first: G

last: Meyer

last: Foucras


title: Response of rice seedlings to the allelochemical juglone

status: Public on Aug 17 2011

city: Tainan

first: Wen-Chang

last: Chi

state: Taiwan

address: No.1, University Road, Tainan City

department: Life Science

country: Taiwan

institute: National Cheng Kung University

summary:
Juglone is phytotoxic and has been widely studied for allelopathic effects, but the molecular mode of action of allelochemicals is not well understood.To gain more insight into cellular responses to juglone, we have taken a large-scale analysis of the rice transcriptome during juglone stress. Exposure to juglone triggered changes in the transcript levels for several genes related to cell rescue and defense, with the majority of these genes potentially associated with chemical detoxification pathways, abiotic stress response pathway, cell wall formation and epigenetic mechanism.
Molecular mechanisms for the allelochemical,juglone, in rice roots

overall_design: Comparison of mock control and  rice seedlings treated with 10mM juglone; Biological replicates: 3 control replicates, 3 juglone-treated replicates.

first: Shin-Feng

last: Fu

first: Tsai-Lien

last: Huang

first: Yun-An

last: Chen

first: Chi-Cien

first: Hao-Jen


title: High-throughput sequencing of small RNAs in Chlamydomonas reinhardtii

status: Public on Sep 30 2011

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from cultures of Chlamydomonas reinhardtii  (in control, phosphate starvation and sulphate starvation conditions). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

overall_design: Small RNA libraries were derived from cultures of Chlamydomonas reinhardtii in control, phosphate starvation and sulphate starvation conditions. Total RNA was isolated using the TriReagent (Molecular Research Center), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Monica

last: Accerbi

first: Pamela

middle: J

last: Green

first: Blake

middle: C

last: Meyers


title: Rice plants (Oryza sativa var. japonica): WT vs. MIT knockdown plant

status: Public on Apr 07 2011

city: Miyagi

first: Yasuhiro

last: Ishimaru

address: 6-3 Aramakiaza-aoba, Aoba-ku, Sendai

country: Japan

institute: Tohoku University

summary: Transcriptional profiling of MIT knockdown plants. MIT is a mitochondrial Fe transporter essential for rice growth and development. The goal was to determine the effects of MIT on global rice gene expression.

overall_design: Control condition experiment, root or shoot of WT vs. MIT knockdown plant. Two replicates each comparison, including a dye swap.


title: Comparison of gene expression of L. reuteri ATCC PTA 6475 at different growth phase in a LDMIII

status: Public on Jan 15 2011

city: Houston

first: Delphine

last: Saulnier

state: TX

address: Feigin Center, Suite 830, 1102 Bates Avenue

department: Pathology

country: USA

institute: Baylor College of Medicine

summary: Comparison of gene expression between L. reuteri ATCC PTA 6475 in LDMIII between early log phase (T8), late log phase (T12) or early stationary phase phase (T16) or late stationary phase (T24)

overall_design: Include 3 biological replicate and dye-swap for each comparison. Reference time point =T8


title: Comparison of gene expression of L. reuteri ATCC 55730 at different growth phase in LDMIII medium

summary: Comparison of gene expression between L. reuteri ATCC  55730 in LDMIII between early log phase (T8), late log phase (T12) or early stationary phase phase (T16) or late stationary phase (T24)


title: Comparative Transcriptional Profiling of Two Rice Genotypes, FR13A and Goda Heenati, Under Submergence Stress

status: Public on Dec 01 2010

city: Wuhan

first: Huaiyang

last: Xiong

address: Eighty one road

country: China

institute: Wuhan University

summary: Most rice (Oryza sativa L.) cultivars die within several days of complete submergence, but some indica cultivars, such as FR13A, can survive up to 2 weeks of complete submergence. In FR13A, a major quantitative trait locus (QTL), named Sub1, provides mature plants with submergence tolerance. However, the Sub1 locus can not confer flooding tolerance during germination to FR13A. Another indica cultivar, Goda Heenati, shows both tolerance to flooding during germination and submergence in mature plants. It was once reported that submergence tolerance in FR13A and Goda Heenati cultivars was controlled by their respective genetic locus. These evidences indicate that tolerance to submergence in these two cultivars may involve differential mechanisms. To gain insight into their putatively differential responses to submergence stress, the Agilent rice genome 4×44 K oligonucleotide microarray was used to explore the transcriptome of FR13A and Goda Heenati under control and submergence-stressed conditions. Two-way ANOVA analysis with Benjamini-Hochberg false discovery rate demonstrated that at an overall P＜0.01 level, 2810, 8207, and 4 probes were significantly regulated for genotype, treatment, and genotype×treatment interaction, respectively. To identify statistically significant differentially expressed genes, a combined criterion of 2-fold or more change and unpaired t-test P value < 0.01 was uesd for both FR13A and Goda Heenati. A total of 504 probes were up-regulated and 592 probes were down-regulated in FR13A under submergence stress. In Goda Heenati, 998 probes were induced and 1186 probes were suppressed by submergence treatment.

overall_design: Gene expression levels in the leaves of rice seedlings submerged for 3 d and the corresponding non-submerged controls were measured using Agilent rice genome 4×44 K oligonucleotide microarray. Three biological replicates were performed for each genotype and treatment. A total of 12 samples were hybridized to 12 arrays.

first: Yangsheng

last: Li


title: Characterizing the role of rice NRAMP5 in Manganese, Iron and Cadmium Transport

status: Public on Feb 03 2012

summary: OsNRAMP5 is involved in iron, manganese and cadmium transport. Goal was to determine the effects of knocking down OsNRAMP5 on global rice gene expression.

overall_design:
Two experiments:
Control condition experiment: root or shoot of WT vs. OsNRAMP5 RNAi plants.
WT Cd treatment experiment: 4 weeks old WT plants grown under 0 or 10uM Cd for two weeks


title: Lactobacillus reuteri strains at different growth phases

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

overall_design: Refer to individual Series


title: Investigating the role of OsPDCD5 in rice programmed cell death by inducible expression

status: Public on Jun 30 2011

city: Shanghai

first: Fan

last: Sun

address: 220 Handan Road

institute: Fudan University

summary:
Overexpression of programmed cell death 5 gene (PDCD5) in tumor cells
enhances apoptosis triggered by growth factor or serum deprivation, and
overexpression of its homolog, OsPDCD5, induces the early death of transgenic plants. In this work, a system of inducible OsPDCD5 expression using a heat shock promoter was developed to study PCD in rice at different developmental stages.The results showed that in three-leaf aged and older seedlings, OsPDCD5 could independently induce PCD. In altered plants, OsPDCD5 expression caused lesion mimic phenotype, abnormal leaf morphology, nuclear condensation, DNA fragmentation, and H2O2 production. But two-leaf aged and younger seedlings seedlings showed no visibly morphological phenotype after OsPDCD5 expression, suggested that young seedlings possessed some mechanism inhibiting OsPDCD5 induced PCD.

overall_design: The transcripts of 24-day-old transgenic Zhonghua 11 seedlings heat-shocked for 6 h (before the appearance of PCD phenotypes) were compared with untreated seedlings using microarray analysis (3-Leaf Group) to study the genes involved in OsPDCD5 induced PCD. The experiment was also performed using 18-day-old seedlings to discover why OsPDCD5 expression did not induce PCD in very young seedlings (2-Leaf Group). RNA samples were extracted using TRIzol (Invitrogen) as described by the manufacturer. Microarray analyses were carried out using a competitive hybridization method using the Agilent microarray system. All procedures were carried out according to the manufacturer's protocols. Briefly, total RNA from each sample was used to synthesize cRNA and was labeled with cyanine-5 (Cy5)- or cyanine-3 (Cy3)-labeled CTP. The labeled cRNAs (including a heat-shocked and a control sample) were competitively hybridized to the Agilent Rice Oligo Microarrays, and then washed. The hybridized slides were scanned using Agilent DNA Microarray Scanner and data points were extracted using Agilent Feature Extraction software. Two comparisons were made between biologically independent samples.

first: Weiwei

last: Qi

first: Jinshui

last: Yang


title: Gene expression profiling of BM-derived dendritic cells reveals important mechanisms associated with predisposition to Staphylococcus infections

status: Public on Oct 01 2011

city: CASTANET TOLOSAN CEDEX

first: Cécile

last: Bonnefont

address: Auzeville B.P. 52627

summary: Background: Staphylococcus aureus is a major pathogen of humans and animals and rapidly emerging antibiotic-resistant strains have further increased the severity of this health issue. Host genetics influence susceptibility to S. aureus infections, and genes determining infection outcome should be identified to analyze immune-based therapies as an alternative to antibiotics. Here, we used outbred animals from a divergent selection on susceptibility towards Staphylococcus infection to explore host immunogenetics. Methodology/Principal Findings: We investigated how dendritic cells respond to heat-inactivated S. aureus and whether dendritic cells from animals with different degree of susceptibility have distinct gene expression profiles. We measured expression levels of 15K probes from in vitro S. aureus-stimulated bone marrow-derived dendritic cells at three different time points (0, 3 and 8 hours) by using Agilent microarrays. Furthermore, a selected number of genes were confirmed by RT-qPCR. Gene signatures of stimulated DCs were obtained and genes involved in inflammatory process and T helper cell polarization were highly up regulated upon stimulation. Moreover, a set of 204 genes were statistically different between susceptible and resistant animals, and grouped them according to their predisposition to staphylococcal infection. Interestingly, a role of classical pathway of Complement and early regulation of inflammation is observed in the resistant line through over expression of C1q and Ido1 genes respectively. On the opposite, over expression of genes in the IL1R pathway in the susceptible animals was noticed. Furthermore, leucocyte extravasation pathway was also found dominant in the susceptible line. Conclusion/Significance: we successfully obtained Staphylococcus aureus associated gene expression of ovine BM-DC in 8 hour kinetics experiment. Distinct transcriptional profiles of dendritic cells obtained from resistant and susceptible lines may explain susceptibility towards S. aureus infections in a broad context. Keywords: Staphylococcus aureus, dendritic cells, mammalian, transcriptome, immunity, mastitis

overall_design: 44 sample records; two-colour dye-swap experimental design

first: M

last: Toufeer

first: CMD

first: E

last: Foulon

first: C

last: Caubet

last: Tasca

first: MR

last: Aurel

first: CR

last: Granié

first: R

last: Rupp

first: G


title: comparison between salmonella wild type 14028s and salmonella mutant prgh in arabidopsis infection.-Transcriptomic analysis of Arabidopsis genes after treatment with Salmonella 14028s and Salmonella type three secretion system (T3SS) mutant prgh

status: Public on Jul 01 2012

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: ra11-01_prgh - comparison between salmonella wild type 14028s and salmonella mutant prgh in arabidopsis infection. - What is the transcriptomic reprogramming after Salmonella infection, What is the importance of the T3SS in the plant infection, Are there differences in gene expression between the 2 bacterial strains? What are the functions of these genes,         - Seedlings treated with S.Typhimurium 14028 WT and St 14028 prgH mutant.Mock treatment done with equal volume of MgCl2.

overall_design: 22 dye-swap - time course,treated vs untreated comparison

first: Heribert

last: Hirt

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Statistical identification of gene association by CID in application of constructing ER regulatory network

status: Public on Jul 10 2009

city: Taipei

first: Fon-Jou

last: Hsieh

address: No. 7, Chung-Shan South Rd

department: Department of obstetrics and gynecology

institute: National Taiwan University

summary: A variety of high-throughput techniques are now available for constructing comprehensive gene regulatory networks in systems biology. In this study, we report a new statistical approach for facilitating in silico inference of regulatory network structure. The new measure of association, coefficient of intrinsic dependence (CID), is model-free and can be applied to both continuous and categorical distributions. When given two variables X and Y, CID answers whether Y is dependent on X by examining the conditional distribution of Y given X. In this paper, we apply CID to analyze the regulatory relationships between transcription factors (TFs) (X) and their downstream genes (Y) based on clinical data. More specifically, we use estrogen receptor alpha (ERalpha) as the variable X, and the analyses are based on 48 clinical breast cancer gene expression arrays (48A). RESULTS: The analytical utility of CID was evaluated in comparison with four commonly used statistical methods, Galton-Pearson's correlation coefficient (GPCC), Student's t-test (STT), coefficient of determination (CoD), and mutual information (MI). When being compared to GPCC, CoD, and MI, CID reveals its preferential ability to discover the regulatory association where distribution of the mRNA expression levels on X and Y does not fit linear models. On the other hand, when CID is used to measure the association of a continuous variable (Y) against a discrete variable (X), it shows similar performance as compared to STT, and appears to outperform CoD and MI. In addition, this study established a two-layer transcriptional regulatory network to exemplify the usage of CID, in combination with GPCC, in deciphering gene networks based on gene expression profiles from patient arrays. CONCLUSION: CID is shown to provide useful information for identifying associations between genes and transcription factors of interest in patient arrays. When coupled with the relationships detected by GPCC, the association predicted by CID are applicable to the construction of transcriptional regulatory networks. This study shows how information from different data sources and learning algorithms can be integrated to investigate whether relevant regulatory mechanisms identified in cell models can also be partially re-identified in clinical samples of breast cancers. AVAILABILITY: the implementation of CID in R codes can be freely downloaded from (http://homepage.ntu.edu.tw/~lyliu/BC/).

overall_design: Total 48 clinical arrays (48A) used in this study can be found in GSE9309. We designed the experiments using a given breast cancer population with clear status of estrogen receptor alpha (ER), which were confirmed by immunochemical staining (If ³10% immunopositive stain is found at tumor section, we designate it as ER(+). Otherwise, it is ER(-). ) in this study.  48A consist of 36A with positive in ER status and of 12A with negative in ER status.


title: Gene expression profiles of two distinct neuronal populations in the neonatal rat spinal cord

status: Public on Mar 31 2008

city: stockholm

first: Jesper

last: Ryge

address: retziusvag 8

department: neuroscience

country: Sweden

institute: karolinska institutet

summary:
Here we compare the gene expression profiles of two distict, fluorescently identified neuronal populations, the motor neruons (MN) and the decending commissural interneurons (dCIN) of the neonatal rat spinal cord isolated with laser microdissection.
These two populations participate in the neuronal networks in the spinal cord where they have destinct functions in shaping (dCINs) and transferring the output to the muscles (MNs) during locomotion.
We wished to determine how the functinal differences in these nerurons are manifested at the gene expression level.
Keywords: Cell type comparison.

overall_design: Neurons were retrogradely labelled with rhodamine through application of the tracer to cut axons followed by incubation in oxygenated Ringer solution. Spinal cord were then snap frozen, cryosectioned and fluorescent single cells were laser dissected into a collector tube to a total of ca. 50-200 cells pr sample.  RNA was then extracted, two round amplified and hybridized to Affymatrix RNU-34 chips.  22 samples were hybridized onto chips, 7 MNs, 7 CINS and 8 MIX.

first: Ann-Charlotte

last: Westerdahl

first: Ole

last: Kiehn


title: Sheep dendritic cells CD26+ and CD26- versus total dendritic cells

status: Public on Jul 23 2010

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

summary:
Transcriptomic profiling of ovine skin lymph dendritic cell subsets CD26+ and CD26- compared to total enriched lymph dendritic cells.
CD26+ and CD26- dendritic cells (DC) from sheep skin lymph were sorted by flow cytometry and were analysed for their transcriptomic profile. We demonstrate that the minor sheep CD26+ skin lymph DC subset shares significant transcriptomic similarities with mouse CD8a+ and human BDCA3+ DC. This allowed the identification of a common set of phenotypic characteristics for CD8a-like DC in the 3 mammalian species, i.e. SIRPlo, CADM1hi, CLEC9Ahi, DEC205hi, XCR1hi. Compared to CD26- DC, the sheep CD26+ DC show (1) potent stimulation of allogeneic naive CD8+ T cells with high selective induction of the Ifn-gamma and Il22 genes; (2) dominant efficacy in activating specific CD8+ T cells against exogenous soluble antigen; (3) selective expression of functional pathways associated to high capacity for antigen cross-presentation.

overall_design: Reference design (total enriched lymph dendritic cells) - Biological replicates: 2 sheep #10081 and #30066

first: Isabelle

last: Schwartz-Cornil

first: Marc

last: Dalod


title: Effect of 3,OC12-HSL on the transcriptome of the ectomycorrhizal fungus Laccaria bicolor S238N

status: Public on Nov 23 2010

city: Champenoux

first: Francis

last: Martin

address: Route d'amance

department: EFPA

summary: Bacteria use small diffusible molecules to communicate and to coordinate population response by a cell density-depend mechanism named quorum sensing (QS). If such a cross-talk was first described between bacterial species, it was recently evidenced that  bacterial QS signal molecules can also be sensed by eukaryotic organisms thus playing as inter-kingdom signalling molecules. Although ectomycorrhizal fungi interact physically and metabolically with myriads of bacterial species in soils, nothing is known about the ability of ectomycorrhiza-associated bacteria to produce QS molecules and the potential impact of these molecules in the interaction. While investigating the potential effect of these molecules on the physiology of the ectomycorrhizal fungus, we found that 3O,C12-HSL also induced an alteration of the transcriptome of L. bicolor S238N.

overall_design: This study used the microarray design as follows: cDNA libraries from pure culture of Laccaria bicolor S238N mycelium and from three stages of L. bicolor S238N sporocarp development (Lb2 library: stipes and caps of 5–10 mm growing sporocarps; Lb3 library: caps of 30– 40 mm mature sporocarps), collected under Douglas ﬁr seedlings grown in a glasshouse, were constructed in the λTriplEx2 vector. The cDNA inserts from bacterial clones were PCR-ampliﬁed and 4992 cDNAs were arrayed from 384-well microtitre plates on Nylon membranes. Three independent biological replicates were performed for the treatment (3,OC12-HSL) and for the control (ethyl acetate)

first: Aurelie

last: Deveau

first: Stephane

last: Uroz

first: Christine

last: Delaruelle

first: Pascale

last: Frey-Klett

first: Peter

last: Martina


title: Gene expression profiles of the egg and synergid cell in rice

city: Mishima

first: Nori

last: Kurata

state: Shizuoka

address: 1111 Yata

institute: National Institute of Genetics

summary: To reveal comprehensive gene expression profiles and their characteristics of the rice egg and synergid cell, we performed cell type-specific microarray analysis using nonenzymatic cell isolation technique. 40 and 50 genes expressed specifically in the egg cell and synergid cell were identified by cluster analysis using microarray results including that of control samples. Furthermore, we found that the differences in the gene expression profiles of the egg cell and the synergid cell were more extensive than previously realized, indicating that these reproductive cells are specified during the short period encompassing the three sequential mitotic nuclear divisions after generation of the megaspore.

overall_design: Gene expression analysis in five samples (egg cell, synergid cell, ovary with or without mannitol treatment, and whole plant) were performed. Three biological replicates were prepared for each sample.

first: Takayuki

last: Ohnishi

first: Hideki

last: Takanashi

first: Mirai

last: Mogi

first: Hirokazu

last: Takahashi

first: Shunsuke

last: Kikuchi

first: Kentaro

last: Yano

first: Takashi

last: Okamoto

first: Masahiro

last: Fujita

first: Nobuhiro

last: Tsutsumi


title: Global gene expression profiles among five independent cytoplasmic male sterile lines.

status: Public on Aug 22 2010

city: Sendai

first: Kinya

last: Toriyama

state: Miyagi

address: Tsutsumidori^Amamiyamachi, Aobaku

department: Graduate School of Agricultural Science

summary: We employed a microarray-based transcriptomic status comparison of rice cytoplasmic male sterile (CMS) lines in order to categorize the nuclear gene expressions upon cytoplasmic substitution. In anthers at the uninucleate and bicellular pollen stages, we found that 8,199 genes significantly changed their expression in at least one of the CMS lines. We categorized the genes into 100 clusters by k-means clustering, and common obvious expression patterns were observed in W11, LD and BT.

overall_design: RNA expression was measured for the anthers at uninucleate and bicellular pollen stages of five CMS lines (BT, CW, LD, W11, WA). T65 was used as the wild-type control. Microarray analysis was performed by three replicates using RNA extracted from independent plants.

first: Sota

last: Fujii


title: Rice expression atlas (5): Anther development (Agilent data)

status: Public on Nov 11 2010

summary:
Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. Decrease of expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several CDKs, cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the deepest and most comprehensive dataset available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed.

Keywords: developmental stage comparison, tissue comparison, platform comparison

overall_design:
Anther development of rice from hypodermal archesporial cells formation to tri-cellular mature pollens were divided into eight stages.
Two biological replicates at each stage were analyzed with Agilent Rice 60mer oligo DNA microarray 4x44K RAP-DB, and total number of samples in this series is 16.
In this series, we analyzed the RNA samples used in GSE13988 for platform comparison.

first: Youko

last: Horiuchi

first: Yayoi

last: Ueda

first: Yoko

last: Mizuta

first: Takahiko

last: Kubo

first: Shinichiro

last: Yamaki

first: Katsutoshi

last: Tsuda

first: Mitsuru

last: Niihama

first: Hirotaka

last: Kato

first: Takako

last: Mochizuki


title: The study of Atlantic cod (Gadus morhua) spleen global gene expression response to intraperitoneal injection with formalin-killed atypical Aeromonas salmonicida.

status: Public on Nov 05 2010

city: St. John's

first: Marije

last: Booman

state: NL

address: 1 Marine Lab Road

department: Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

summary: This study was performed to validate the newly developed CGP Atlantic cod 20K oligonucleotide microarray. Atlantic cod (Gadus morhua) received an intraperitoneal injection of either formalin-killed, atypical Aeromonas salmonicida (Asal) or PBS and transcriptional profiles of spleen tissues from Asal-injected fish were compared to those from pre-injection control fish and PBS-injected control fish. Gene expression profiles resulting from this study were compared to those from suppression subtractive hybridization library studies, that were previously performed on the same samples, and to literature. Gene expression patterns of single genes were confirmed by QPCR analysis. This study has shown that the newly developed CGP Atlantic cod 20K oligo microarray platform is a valuable tool for cod genomic research.

overall_design: Fish were assigned to 1 of 3 groups: Asal group, PBS group or 'undisturbed control' group (the latter were not handled during the experiment). These groups were kept in 3 separate tanks. For the test samples, RNA was used from individual spleen samples that were taken from 6 fish from each of 4 treatment groups: PBS group pre-injection (0H PBS), Asal group pre-injection (0H Asal), PBS group 24 hours post-injection (24HPI PBS) and Asal group 24 hours post-injection (24HPI Asal). All test samples were labeled with AlexaFluor 647. For the universal reference sample, RNA from 31 'undisturbed control' fish was pooled, with each individual contributing an equal amount, and labeled with AlexaFluor 555. Each individual test sample was hybridized together with the universal reference sample on an array. For one sample from the 0H PBS group the array failed. This study therefore includes 6 biological replicates for 0H Asal, 24HPI Asal and 24HPI PBS groups and 5 biological replicates for the 0H PBS group.

first: Tudor

last: Borza

first: Charles

middle: Y

last: Feng

first: Tiago

middle: S

last: Hori

first: Brent

last: Higgins

first: Jennifer

middle: R

last: Hall

first: Marlies

last: Rise

first: A

middle: K

last: Gamperl

first: Sophie

last: Hubert

last: Kimball

first: Stewart

last: Johnson

first: Sharen

last: Bowman

first: Matthew

middle: L


title: Utricle Neomycin Timecourse

status: Public on Feb 01 2007

city: Saint Louis

first: Kara

last: Powder

state: MO

address: 4566 Scott Ave

department: Genetics

institute: Washington University in St Louis

summary:
Much of human hearing loss is caused by loss of auditory hair cell (HC) function.  Mammals cannot regenerate these essential mechanoelectrical transducers of sound.  However, birds have retained the ability to regenerate HCs from surrounding supporting cells. To better understand hair cell regeneration, we have expression profiled the sensory epithelia from chicken cochleae and utricles.  Pure sensory epithelia, consisting of HCs plus supporting cells, were damaged with either neomycin or laser treatment.  Changes in gene expression at various points during regeneration were compared to undamaged control cultures on a custom microarray that interrogates the vast majority of transcription factor (TF) genes.   These experiments involved multiple biological samples and hundreds of microarray comparisons.
Keywords: timecourse

platform_organism:
Gallus gallus
Homo sapiens
Mus musculus

overall_design: Utricle sensory epithelia was antibiotic treated and allowed to recover for 0hr, 24hr, or 48hr.  There are 3 biological samples per timepoint, and experiments include technical replicates as well as dye-switches for a total of 65 microarrays.

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