title: Resistance gene-dependent responses in rice to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae

status: Public on Nov 22 2011

city: Ames

first: PLEXdb Curator

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: TITLE: Transcriptional profiling of Rgene-mediated responses in rice    PROJECT DESCRIPTION: The dominant gene Xa7 and the recessive gene xa5 of  rice confer resistance to several races of the bacterial blight pathogen  Xanthomonas oryzae pv. oryzae (Xoo). To reveal the modes of action and  the defense responses these genes initiate, we decided to obtain the  global transcriptional profiles of the rice cultivars IRBB7, IRBB5  (which harbor Xa7 and xa5, respectively) and IR24 undergoing early  infection by the Xoo Race 2 strain PXO86. Both IRBB7 and IRBB5 are  resistant to PXO86 (which carry the corresponding avirulence genes  avrXa7 and avrxa5), whereas IR24 is susceptible. We inoculated by vacuum  infiltration the three rice cultivars ten days after seed germination  (or 2 weeks after sowing) and collected inoculated tissue at 5 different  timepoints within the first day after inoculation. The transcriptional  profiles obtained will provide valuable insight into the similarities  and differences between incompatible interactions mediated by a dominant  and a recessive Rgene, in comparison to a compatible interaction.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  David O Nino-Liu.  The equivalent experiment is OS4 at PLEXdb.]

overall_design: genotype: IR24 - time: 0 hai(3-replications);  genotype: IR24 - time: 3 hai(3-replications);  genotype: IR24 - time: 6 hai(3-replications);  genotype: IR24 - time: 12 hai(3-replications);  genotype: IR24 - time: 24 hai(3-replications);  genotype: IRBB5 - time: 0 hai(3-replications);  genotype: IRBB5 - time: 3 hai(3-replications);  genotype: IRBB5 - time: 6 hai(3-replications);  genotype: IRBB5 - time: 12 hai(3-replications);  genotype: IRBB5 - time: 24 hai(3-replications);  genotype: IRBB7 - time: 0 hai(3-replications);  genotype: IRBB7 - time: 3 hai(3-replications);  genotype: IRBB7 - time: 6 hai(3-replications);  genotype: IRBB7 - time: 12 hai(3-replications);  genotype: IRBB7 - time: 24 hai(3-replications)

first: David

middle: O

last: Nino-Liu

first: Adam

middle: J

last: Bogdanove


title: Expression data from transgenic rice with anti-OsPDCD5

status: Public on Nov 01 2011

city: shanghai

first: Mengfei

last: Yang

address: Handan Road 220

country: China

institute: Fudan university

summary:
Environmental stresses influence the growth of plants and the productivity of crops. Salinity is one of the most important abiotic stresses for agricultural crops. PCD is induced by various biotic and abiotic stresses in algae and higher plants, including high salinity treatment. OsPDCD5, an ortholog to mammalian-programmed cell death 5, is up-regulated under low temperature and NaCl treatments.
We found that the transgenic rice which constitutively expressed anti-OsPDCD5 increased salt stress tolerance in unique ways. By using the Rice Genome Microarray, we identiﬁed target genes that were regulated in transgenic rice plants by anti-OsPDCD5.

overall_design: Leaf tissues of 2-week-old transgenic and nontransgenic seedlings (10 plants each) before 200mM NaCl treatment, 20mins and 3 hours after 200mM NaCl treatment, respectively, were selected.

first: Jinshui


title: A global analysis of QTLs for expression variations in rice shoot at early seedling stage

status: Public on Jun 24 2011

city: Wuhan

first: Jia

last: Wang

state: Hubei

address: Shizishan Street #1

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University (HZAU)

summary:
Analyses of QTLs for expression levels (eQTLs) of the genes reveal genetic relationship between expression variation and the regulator, thus unlocking the information for identifying the regulatory network. Oligo-nucleotide expression microarrays hybridized with RNA can simultaneously provide data for molecular markers and transcript abundance. In this study, we used Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice shoots at 72 h after germination from 110 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63.
Totally 1,632 single feature polymorphisms (SFPs) plus 23 PCR markers were identified and placed into 601 recombinant bins, spanning 1,459 cM in length, which were used as markers to genotype the RILs. We obtained 16,372 expression traits (e-traits) each with at least one eQTL, resulting in 26,051 eQTLs in total, including both cis- and trans-eQTLs. We also identified 171 eQTL hotspots among rice genome, each of which controls transcript variations of many e-traits. Gene Ontology analysis revealed enrichment of certain functional categories of genes in some of the eQTL hotspots. In particular, eQTLs for e-traits involving DNA metabolic process was significantly enriched in several eQTL hotspots on chromosomes 3, 5 and 10. Several transcription factors colocalizing with cis-eQTLs showed significant correlations with hundreds of e-traits, indicating possible co-regulation. We also detected correlations between the QTLs for shoot dry weight and eQTLs, revealing possible candidate genes for the trait. These results provided the clues for identification and characterization of regulatory network in the whole genome at the transcriptional level.

overall_design: To dissect the genetic variation between the two rice indica varieties Minghui 63 and Zhenshan 97, a total of 110 RILs from Minghui 63 and Zhenshan 97 and parents were sampled. And the Affymetrix Genechip rice Genome Array was used to investigate their dynamic transcript levels. Two independent biological replicates were sampled from each RIL, and three replicates for each parent.resulting in a dataset of 226 microarrays.

first: Huihui

last: Yu

first: Weibo

last: Xie

first: Yongzhong

last: Xing

first: Sibin

first: Caiguo

last: Xu

first: Xianghua

last: Li

first: Jinghua

last: Xiao

first: Qifa

last: Zhang


title: DNA microarray data from transgenic rice KMD and its parent XS11

status: Public on Oct 26 2011

city: Beijing

first: Jie

last: Zhao

address: No. 2 Yuan Ming Yuan West Street

institute: Institute of Plant Protection, Chinese Academe of Agricultural Sciences

summary: KMD is genetically engenered to be highly resistant to lepidopteran pests through expressing a synthetic cry1Ab gene and its parent non-transgenic rice is Xiushui 11 (XS11). Many unintended effects have been discovered in KMD. We used microarrays to study the molecular basis  for unintended effects of KMD rice.

overall_design: Samples were collected from both KMD and XS11 for RNA extraction and hybridization on Affymetrix microarrays. We selected differentially expressed genes hoping to clarify the molecular basis for unintended effects in KMD.

first: Fangjun

last: Qi

first: Zhi

last: Liu


title: Methanol is an endogenous elicitor molecule upon senescence of detached rice leaves

status: Public on Jan 03 2011

city: Gwangju

first: Young Soon

last: Kim

address: 300 Youngbong-dong

department: Bioenergy Research Center

country: South Korea

institute: Chonnam National University

summary: During senescence of detached rice leaves, tryptophan (Trp) and Trp-derived secondary metabolites such as serotonin and 4-coumaroylserotonin accumulated in concert with methanol (MeOH) production. This senescence-induced MeOH induction was closely associated with levels of pectin methylesterase (PME)1 mRNA and PME enzyme activity. Exogenous challenge of detached rice leaves with 1% MeOH accelerated Trp and serotonin biosynthesis with induction of the corresponding genes. No other solvents including ethanol resulted in a Trp-inducing effect. This MeOH-induced Trp synthesis was positively regulated by abscisic acid but negatively regulated by cytokinin, suggesting hormonal involvement on the action of MeOH. Endogenous overproduction or suppression of MeOH either by PME1 overexpression or RNAi gene silencing revealed that PME1 overexpressing lines produced twofold higher Trp levels with elevated Trp biosynthetic gene expression, whereas RNAi lines showed twofold reduction in Trp level in healthy control rice leaves, suggesting that MeOH acts as an endogenous elicitor to enhance Trp biosynthesis. Among many transcription factors induced following MeOH treatment, the WRKY family showed significant induction patterns of which WRKY14 appeared to play a key regulatory role in MeOH-induced Trp and Trp-derived secondary metabolite biosynthesis.

overall_design: Total RNAs were extracted from the detached rice leaves with 1% MeOH or distilled water for 1 d, and gene expression was compared between the two groups with two replicates. DW, detached leaves in distilled water for 1 day; MeOH (2-replications), methanol treated detached leaves at the same time point as control. 2 sets of separately normalized data; DW-MeOH(1) and MeOH(2).

first: Kiyoon

last: Kang

first: Sangkyu

last: Park

first: Uyanga

last: Natsagdorj

first: Young

middle: S

first: Kyoungwhan

last: Back


title: Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves

status: Public on Mar 24 2011

first: Wenying

address: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice.

overall_design:
we generate rice diurnal gene expression profiles of seedling leaves and flag leaves using 57K Affymetrix rice whole genome array.
keywords: rice (Oryza sativa L.), seedling leaves, flag leaves, diurnal,  molecular functions, microarray

first: W

first: M

first: Z

last: Yang

first: G

last: Chen

first: H

last: Guo

first: Q

last: Qian

last: Su

first: Y

last: Xue


title: Transcription analysis of wild-type and chuR Bacteroides thetaiotaomicron genes in the mouse cecum

status: Public on Jan 01 2011

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

state: MI

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

country: USA

institute: University of Michigan Medical School

summary: The large-scale application of genomic and metagenomic sequencing technologies has yielded a number of insights about the metabolic potential of symbiotic human gut microbes. Bacteria that colonize the mucosal layer that overlies the gut epithelium have access to highly-sulfated polysaccharides (i.e., mucin oligosaccharides and glycosaminoglycans), which they could potentially forage as nutrient sources. To be active, sulfatases must undergo a critical post-translational modification catalyzed in anaerobic bacteria by the AdoMet enzyme anSME (anaerobic Sulfatase-Maturating Enzyme). In the present study, we have tested the role of this pathway in the prominent gut symbiont Bacteroides thetaiotaomicron, which possesses more predicted sulfatases (28) than in the human genome and a single predicted anSME. In vitro studies revealed that deletion of its anSME (BT0238) results in loss of sulfatase activity and impaired ability to use sulfated polysaccharides as carbon sources. Co-colonization of germ-free animals with both isogenic strains, or invasion experiments involving the introduction of one then the other strain, established that anSME activity and the sulfatases that are activated via this pathway, are important fitness factors for B. thetaiotaomicron, especially when mice are fed a simple sugar diet that requires this saccharolytic bacterium to adaptively forage on host glycans as nutrients. Whole genome transcriptional profiling of wild-type and the anSME mutant in vivo revealed that loss of this enzyme alters expression of genes involved in mucin utilization and that this disrupted ability to access mucosal glycans likely underlies the observed dramatic colonization defect. Comparative genomic analysis reveals that 100% of 46 fully sequenced human gut Bacteroidetes contain homologs of BT0238 and genes encoding sulfatases, suggesting that this is an important and evolutionarily conserved feature.

platform_organism:
Bacteroides thetaiotaomicron
Streptococcus thermophilus
Lacticaseibacillus casei
Lactobacillus delbrueckii
Bifidobacterium animalis
Agathobacter rectalis
Bifidobacterium longum

overall_design: Three replicate samples from 4 different biological treatment groups: 1. Wild-type B. thetaiotaomicron from the cecum of gnotobiotic mice fed a simple-sugar diet; 2. chuR mutant B. thetaiotaomicron from the cecum of gnotobiotic mice fed a simple-sugar diet; 3. Wild-type B. thetaiotaomicron from the cecum of gnotobiotic mice fed a plant-rich diet; 4. chuR mutant B. thetaiotaomicron from the cecum of gnotobiotic mice fed a plant-rich diet.

middle: C

first: Jeffrey

middle: I

last: Gordon


title: Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice

status: Public on Jun 10 2011

city: New Delhi

first: Sanjay

last: Kapoor

state: Delhi

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

summary: Background – In flowering plants, the anther is the site of male gametophyte development. Two major events in the development of the male germline are meiosis and the asymmetric division in the male gametophyte that gives rise to the vegetative and generative cells, and the following mitotic division in the generative cell that produces two sperm cells. Anther transcriptomes have been analyzed at progressive stages of development by using microarray and sequence by synthesis technologies to identify genes that regulate anther development. Here we have carried out a comprehensive analysis of rice anther transcriptomes at four distinct stages of development with a focus to identify regulatory components contributing to male meiosis and germline development. Further, these transcriptomes have been compared with transcriptomes of 10 stages of rice vegetative and seed development to identify genes that express specifically during anther development. Results - To understand the molecular processes that lead to male gametophyte development, transcriptome profiling of four stages of anther development in rice [pre-meiotic (PMA), meiotic (MA), anthers at single-celled (SCP) and tri-nucleate pollen (TPA)] was conducted. Around 22,000 genes were found to be expressed in at least one of the anther developmental stages, with the highest number in MA (18,090) and lowest (15,465) in TPA. Comparison of these transcriptome profiles to an in-house generated microarray-based transcriptomics database comprising of 10 stages/tissues of vegetative as well as reproductive development in rice resulted in the identification of 1,000 genes that are specifically expressed in anther stages. Of them the expression of 453 genes was found to be specific to TPA, whereas 78 and 184 genes were expressed specifically in MA and SCP. Gene ontology and pathway analysis of specifically expressed genes revealed that transcription factors and protein folding, sorting and degradation pathway genes dominated in MA, whereas in TPA, those coding for cell structure and signal transduction components were in abundance. Interestingly, about 50% of the genes with anther-specific expression have not been annotated so far. Conclusions - These data not only provide the transcriptome constituents of four landmark stages of anther development but also identify genes that express exclusively in these stages and therefore may contribute to specific aspects of anther and/or male gametophyte development in rice. Moreover, these gene sets assist in building a deeper understanding of underlying regulatory networks and in selecting candidates for gene function validation.

overall_design: Overall twelve samples were analyzed representing four anther development stages, with three replicates of each stage.

first: Priyanka

last: Deveshwar

first: William

middle: D

last: Bovill

first: Rita

last: Sharma

first: Jason

middle: A

last: Able


title: Expression data from transgenic rice with OsEATB

status: Public on Jul 01 2011

city: Shanghai

first: weiwei

last: qi

address: 220#Handan road

summary: Rice ethylene-response AP2/ERF factor OsEATB restricts internode elongation by down-regulating gibberellin biosynthetic gene

overall_design: Leaf tissues of 4-leaf-old transgenic and nontransgenic seedlings (10 plants each), respectively, were selected.

first: Weiwei

last: Qi

first: Jinshui


title: Comparsion of gene expression profile in polaris (pola) mutant lines and its POLARIS (POLA) wild-type at meiotic and ripening stages

status: Public on Dec 01 2010

city: Kunming

first: LI

last: JUAN

state: Yunnan

address: Black Dragon Pool

department: Rice Research Institute

institute: Yunnan Agricultural University

summary: To assess the role of POLA in relation to ovule development, embryogenesis and endosperm development, we analyzed gene expression profiles by using microarray. Compared to the wild-type plants, several groups of transcription factors in the pola mutant plants and POLA RNAi lines showed up- or down-regulation at meiotic stage and ripening stages of floral development. Specifically, we confirmed significant changes of up- or down-regulation in some genes required for several biological processes, such as biosynthesis, transport, signal transduction, and degeneration of hormone, sugar, starch, fatty and lipid, protein and amino acid. These results supported that MADS protein POLA could function both as a transcriptional activator and repressor, directly and/or indirectly interacted with dozens of potential target genes involved in  developmental and hormonal pathways.

overall_design: To perform microarray analysis, the samples were pooled by 20 panicles from 10 individual plants at meiotic and ripening stage. For meiotic stage RNA sample, panicle of pola mutant were prepared at early to late meiotic stage, and panicle of POLA RNAi line(T2) were prepared at ten to fifteen days after pollination stage for ripening stage RNA sample.

first: Lee

last: Dong Sun

first: Chen

last: Li Juan

first: Li

last: Cheng Yun

first: Liu

last: Yong Sheng

first: Tan

last: Xue Lin

first: Lu

last: Bao-Rong

last: Juan

first: Gan

last: Shu Xian

first: Kang

last: Sang Gu

first: Snh

last: Hak Soo

first: Zhu

last: You Yong


title: Oryza sativa genes expressed in the early compatible interaction with root-knot nematode (affy_meloidogyne_rice)

status: Public on Sep 25 2011

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

summary:
affy_meloidogyne_rice - affy_meloidogyne_rice - Plant-parasitic nematodes cause profound economic losses to global agriculture with the obligate sedentary endoparasitic varieties; amongst them the cyst and Root Knot Nematode (RKN) species are the most damaging. Meloidogyne graminicola is a RKN mainly found in the monocotyledous plants. In the compatible interaction with Oryza sativa, M. graminicola induces the characteristic formation of hook-like galls resulting from the redifferentiation of root cells into multinucleate giant cells. In order to understand the global transcriptome changes occurring during infection, several recent microarray studies on root knots have demonstrated complex changes in host plant gene expression in response to infection. However, to our knowledge, all these transcriptome studies were performed on dicotyledous plants. A histological study enabled us to observe hyperplasia and hypertrophy of the surrounding cells leading to the formation of hook-like galls. We also investigated the plant response to M. graminicola by carrying out a global analysis of gene expression during gall formation in rice, using giant cell-enriched root tissues at an early stage (2dpi) and a latter stage (4dpi) of gall development.-Oryza sativa (var. Nipponbare) seedlings were grown on 6 cm3 SAP substrate completed with diluted Hoaglands solution (Reversat et al., 1999). Culture units were placed in a growth chamber illuminated with fluorescent tubes 9/24 h and maintained at 23°C for 5 days before being inoculated with a 100 J2-stage juveniles M. graminicola. One day after inoculation (dai), the rice seedlings were immersed in de-ionised water to remove all J2s that had not penetrated the roots and allowing synchronization of the infection. Each seedling was transferred to a hydroponic mini chamber (Reversat et al., 2004). Sampling was performed at 2 and 4 dai and each of them contained galls from 70 infected plants, they were then hand-dissected, frozen in liquid-nitrogen and stored at -80°C. As reference samples, uninfected meristematic root fragments were dissected from seedlings grown under the same conditions. Each sample was replicated 3 times.

Keywords: normal vs disease comparison,time course

overall_design: 9 arrays - rice

first: Stephanie

last: Huguet

first: Stéphane

last: Bellafiore

first: Sandrine

last: Balzergue

first: Marie-Laure

middle: L

last: Martin-Magniette


title: genome-wide gene expression profiling of rice pollen in defferent developmetn stages

status: Public on Mar 18 2011

first: liqin

last: wei

address: 20 nanxincun, Xiangshan, Haidian distict

department: Research Center for Molecular & Developmental Biology

institute: Institute of Botany, Chinese Academy of Sciences

summary:
Pollen development from the microspore involves a series of coordinated cellular events, and the resultant mature pollen is specialized in function that it can quickly germinate and produces a polar-growth pollen tube derived from the vegetative cell to deliver two sperms for fertilization. Understanding the molecular program underlying pollen development and germination still remains a major challenge for plant biology. We used Affymetrix GeneChip Rice Genome Array to comprehensively analyzed the dynamic changes in the transcriptomes of rice pollen at five sequential developmental stages from microspores to germinated pollen. Among the 51,279 transcripts on the array, we found 25,062 pollen-preferential transcripts, among which 2,203 were development stage-enriched. The diversity of transcripts decreased greatly from microspores to mature and germinated pollen, whereas the number of stage-enriched transcripts displayed a U-type change, with the lowest at the bicellular pollen stage; and a transition of overrepresented stage-enriched transcript groups associated with different functional categories, which indicates a shift in gene expression program at the bicellular pollen stage. About 54% of the now-annotated rice F-box protein genes were expressed preferentially in pollen. The transcriptome profile of germinated pollen was significantly and positively correlated with that of mature pollen. Analysis of expression profiles and coexpressed features of the pollen-preferential transcripts related to cell cycle, transcription, the ubiquitin/26S proteasome system, phytohormone signalling, the kinase system and defense/stress response revealed five expression patterns, which are compatible with changes in major cellular events during pollen development and germination. A comparison of pollen transcriptomes between rice and Arabidopsis revealed that 56.6% of the rice pollen preferential genes had homologs in Arabidopsis genome, but 63.4% of these homologs were expressed, with a small proportion being expressed preferentially, in Arabidopsis pollen. Rice and Arabidopsis pollen had non-conservative transcription factors each. These results supply novel insights into the molecular program and key components of the regulatory network regulating pollen development and germination.

KEYWORDS: rice (Oryza sativa L.), pollination and fertilization, stigma, molecular functions, signaling, microarray, stress response

overall_design: we generate rice pollen gene expression profiles through comparing genome-wide expression patterns of 5 development-stage pollen grains (uninucleate microspores, bicellular pollen, immature tricellular pollen, mature pollen and germinated pollen grains ) with rice callus cells, roots and leaves by using 57K Affymetrix rice whole genome array.

first: Liqin

last: Wei

first: Wenying

last: Xu

middle: Y

last: Deng

first: Zhen

last: Su

first: Yongbiao

last: Xue

first: Tai

last: Wang


title: Expression of PTTG1 is associated with aggressive clear cell RCC

status: Public on Dec 31 2010

city: Grand Rapids

first: Bin

middle: Tean

last: Teh

address: 330 Bostwick Av

department: Cancer Genetics

institute: Van Andel Institute

summary: The pituitary-tumor transforming gene (PTTG1) is a recently discovered oncogene implicated in the malignant progression of a number of neoplasms. It has been shown to drive both endocrine and non-endocrine malignancies, but has not yet been studied in the context of renal cell carcinoma. Here we show that PTTG1 is frequently amplified and overexpressed in clear cell renal cell carcinoma, the most common form of kidney cancer. Clear cell RCC (ccRCC) is cytogenetically characterized by deletion of chromosome 3p, harboring the von-Hippel Lindau tumor suppressor gene, and amplification of chromosome 5q. The significance of copy number gain of chromosome 5 has to date remained a mystery, but is presumably the location of oncogenes that play an important role in ccRCC development or progression. The PTTG1 oncogene maps to chromosome 5q and shows frequent copy number gain in clear cell RCC, and is significantly overexpressed in tumor tissue relative to adjacent normal kidney. Furthermore, we have established a functional role for PTTG1 in ccRCC tumorigenesis and progression. PTTG1 ablation significantly reduces both the tumorigenic ability of ccRCC cells in vitro and in vivo and the invasive ability of these cells in vitro. An analysis of PTTG1 regulatory targets supports its role in the progression of localized ccRCC to invasive and metastatic disease, an idea further substantiated by PTTG1’s clinical correlation with high grade and high stage tumors and its association with poor prognosis. PTTG1-dependent overexpression of the Rho-GEF ECT2, another proto-oncogene, is observed in a number of ccRCC cell lines, and ECT2 overexpression correlates with PTTG1 overexpression, high stage, high grade, and poor prognosis in human ccRCC tumors. As GEF’s have been promoted as viable drug targets for targeted cancer therapeutics, the relationship between the PTTG1 and ECT2 oncogenes may be able to be exploited for the treatment of this disease.

overall_design: SNP data on 74 ccRCC and 16 normal renal tissue samples were used to profile the cytogenetic gains or losses. The most frequent gains or losses were identified and gene expression data were then used to pinpoint the genes for further study.

first: Zhongfa

last: Zhang

first: Karl

last: Dykema


title: Affymetrix SNP array data for Japanese schizophrenia samples

status: Public on Jun 13 2011

city: Wako-city

first: Kazuo

last: Yamada

state: Saitama

address: 2-1 Hirosawa

country: Japan

institute: RIKEN Brain Science Institute

summary:
Genome-wide association study (GWAS) was performed in 120 patient-parents trio samples from Japanese schizophrenia pedigrees
ABSTRACT: Schizophrenia is a devastating neuropsychiatric disorder with genetically complex traits.  Genetic variants should explain a considerable portion of the risk for schizophrenia, and genome-wide association study (GWAS) is a potentially powerful tool for identifying the risk variants that underlie the disease.  Here, we report the results of a three-stage analysis of three independent cohorts consisting of a total of 2,535 samples from Japanese and Chinese populations for searching schizophrenia susceptibility genes using a GWAS approach.  Firstly, we examined 115,770 single nucleotide polymorphisms (SNPs) in 120 patient-parents trio samples from Japanese schizophrenia pedigrees.  In stage II, we evaluated 1,632 SNPs (1,159 SNPs of p < 0.01 and 473 SNPs of p < 0.05 that located in previously reported linkage regions).  The second sample consisted of 1,012 case-control samples of Japanese origin.  The most significant p value was obtained for the SNP in the ELAVL2 [(embryonic lethal, abnormal vision, Drosophila)-like 2] gene located on 9p21.3 (p = 0.00087).  In stage III, we scrutinized the ELAVL2 gene by genotyping gene-centric tagSNPs in the third sample set of 293 family samples (1,163 individuals) of Chinese descent and the SNP in the gene showed a nominal association with schizophrenia in Chinese population (p = 0.026).    The current data in Asian population would be helpful for deciphering ethnic diversity of schizophrenia etiology.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

SUPPLEMENTARY FILES:
CEL files were processed by manufacture's protocol.
Genotype data were analyzed with the GeneSpring GT (Varia) 2.0 software package developed by Agilent Technologies (Santa Clara, CA).
Matrix tables for the Genetic programs were produced (Linkage format: http://bioinformatics.med.utah.edu/~alun/software/docs/linkage.html)
File 1: Matrix file_SNP_Map.txt
File 2: Matrix file_Family_Information.txt
File 3: Matrix file_Pedigree_Format.txt (Genotyping data of Linkage format)
Transmission disequilibrium test was performed using the R program
(http://www.r-project.org).
File 4: Matrix file_results.txt

first: Yoshimi

last: Iwayama

first: Eiji

last: Hattori

first: Kazuya

last: Iwamoto

first: Tomoko

last: Toyota

first: Tetsuo

last: Ohnishi

first: Hisako

last: Ohba

first: Motoko

last: Maekawa

first: Tadafumi

last: Kato

first: Takeo

last: Yoshikawa


title: Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice

status: Public on Dec 23 2010

first: pan

last: yajiao

address: Zhongguancun South Street No.12

institute: The chinese academy of agriculture sciences

summary: Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements.

overall_design: In this study, the gene expression patterns across six tissues including leaves and roots at tillering stage and panicle elongation stage, leaves and young panicle at booting stage ( TL: leaves at tillering stage; TR: roots at tillering stage; PL: leaves at panicle elongation stage; PR: roots at panicle elongation stage; BP: young panicle at booting stage; BL: leaves at booting stage) were characterized by using the Affymetrix rice microarray platform based on a drought tolerant rice line derived from IR64.

first: Di

first: Yajiao

last: Pan

first: Xiuqin

last: Zhao

first: Linghua

last: Zhu

first: Lijun

first: Binying

last: Fu

first: Zhikang

last: Li


title: Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays and 16 ovarian tumors on 500K SNP arrays

status: Public on Dec 16 2010

city: South San Francisco

first: Jinfeng

last: Liu

state: CA

address: 1 DNA Way, MS93

department: Bioinformatics and Computational Biology

institute: Genentech Inc.

summary:
Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays

Thirty-six ovarian tumors were profiled for copy-number alterations with the Affymetrix 100K Mapping Array.

Copy number profiling of 36 ovarian tumors on Affymetrix 500K SNP arrays

Sixteen ovary tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array.

overall_design:
Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site.  The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1).

Affymetrix 500K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization.  Forty-eight normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) and analyzed at the same time.  One CEL file for each set (Sty and Nsp) with the median signal intensity across the set was selected as the reference array.  The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows.  For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set.  For Chromosome X, the average of the 20 normal female samples was used.   Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site.  The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1).

first: Zora

last: Modrusan

first: Richard

last: Neve

first: Peter

last: Haverty

first: Ingrid

last: Wertz


title: Gene expression and SNP profiling discriminates chromophobe renal cell carcinoma and oncocytoma

status: Public on Feb 02 2011

city: GrandRapids

first: Naga Manjari

last: Vadlapatla

address: 333 Bostwick Avenue Northeast

institute: Vanandel research Institute

summary: Gene expression profiles, high-throughput SNP genotyping, and pathway analysis effectively distinguish chRCC from oncocytoma.  We have generated a novel transcript predictor that is able to discriminate between the two entities accurately, and which has been validated both in an internal and an independent data-set, implying generalizability.  A cytogenetic alteration, loss of chromosome 1p, common to renal oncocytoma and chRCC has been identified, providing the opportunities for identifying novel tumor suppressor genes and we have identified a series of immunohistochemical markers that are clinically useful in discriminating chRCC and oncocytoma.

overall_design: Oncocytoma and Chromophobe RCC samples -  SNP chip analysis

first: Manjari


title: Expression comparasion of rice seedlings of Osabl1 mutant and WT under ABA treatment

status: Public on Oct 13 2011

first: Xi

last: Yang

address: Fenglin Road, 300

summary: Expression profiles of seedling roots of rice mutant Osabl1 and wild-type under ABA treatment

overall_design: Mutant and wild-type expression profiling were compared and each has two biological repeats.

first: Hongwei

last: Xue

first: Yanan

first: Liangjiao


title: Temporal regulatory role of miR156 during leaf development

status: Public on Oct 26 2010

first: Kabin

last: Xie

address: Shizi Shan Street

institute: Huazhong Agriculture University

summary: The highly conserved plant microRNA, miR156, is an essential regulator for plant development. We found miR156 changed gradually during leaf development. To find how miR156 regulated genes temporally, we analyzed the transcriptome of old and young leaves from miR156-overexpressed and wild type plants. The results show that the gradual increase of miR156 regulates temporal changes of numerous gene expressions during leaf development.

overall_design: To identify genes whose expressions are affected or indirectly regulated by miR156, Affymetrix rice DNA chips were used to check the transcriptomes of old (Leaf 3) and young (Leaf 6) leaves from miR156 over-expression lines and wild type at the tillering stage. In this study, leaves on each tiller were numbered according to its emerging order, with L1 indicating the first developed leaf. Three wild type plants and three independent miR156-overexpressed plants were used for transcriptome analysis by microarray hybridization.

first: Xin

last: Hou

first: Lizhong

last: Xiong


title: Identification of Rhizome-Specific Genes by Genome-wide Differential Expression Analysis in Oryza longistaminata

status: Public on Oct 31 2010

city: beijing

first: ting

last: zhang

state: beijing

address: zhongguancun south street 12

institute: Chinese Acadamy of agricultural science

summary:
The Oryza longistaminata is a perennial wild rice species with AA genome, which characterized by the presence of rhizomatous stem. The rhizomatousness trait in rice was previously identified quantitatively controlled by many genes, but the molecular mechanism related to the rhizome initiation and elongation is still unknown. In this study, the specific gene expression patterns across five tissues in O. longistaminata, especially in the rhizome were characterized by using the Affymetrix rice microarray platform, the rhizome-specific expressed genes and its corresponding regulatory were further analyzed. The different gene sets were determined exclusively expressed in five tissues; strikingly 58 genes with functions related to transcription regulation and cell proliferation were identified as prevalent sets in rhizome tip, of them, several genes were functionally involved in tiller initiation and elongation. And a set of genes were differentially regulated in the rhizome tip relative to shoot tip, the predominant repressed genes are involved in photosynthesis, while genes related to phytohormone and the gene families with redundancy function were obviously differentially regulated. Several cis-regulatory elements, including CGACG, GCCCORE, GAGAC and a Myb Core, were highly enriched in rhizome tip or internode, and two cis-elements such as RY repeat and TAAAG, which implicated in the ABA signaling pathway, were found overrepresented in the rhizome tip in comparison with shoot tip. A few rhizome-specific expressed genes were co-localized on the rhizome-related QTLs regions, indicating these genes may be good functional candidates for the rhizome related gene cloning.
The whole genome profiling of oryza longistaminata indicated that a very complex gene regulatory network underlies rhizome development and growth, and there might be an overlapping regulatory mechanism in the establishment of rhizome and tiller. Phytohormone such as IAA and GA are involved in the signaling pathway in determining rhizome. Several cis-elements enriched in rhizome and the identified rhizome-specific genes co-localized on the rhizome-related QTL intervals provide a base for further dissection of the molecular mechanism of rhizomatousness

overall_design: In this study, the specific gene expression patterns across five tissues including rhizome tip (RT, distal 1 cm of the young rhizome), rhizome internodes (RI), shoot tip (ST, distal 5 mm of the tiller after removing all leaves), shoot internodes (SI) and young leaf (YL) in O. longistaminata, especially in the rhizome were characterized by using the Affymetrix rice microarray platform.

first: Feng-Yi

last: Hu

first: Di

last: Wang

first: Xiu-Qin

first: Ting

last: Zhang

first: Hai-Xi

last: Sun

first: Ling-hua

first: Fan

first: Li-Juan

first: Qiong

first: Da-Yun

last: Tao

first: Bin-Ying

first: Zhi-Kang


title: Rice expression atlas (1): Anther development

status: Public on Nov 11 2010

city: Mishima

first: Nori

last: Kurata

state: Shizuoka

address: 1111 Yata

institute: National Institute of Genetics

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.
Three or four biological replicates at each stage were analyzed with Affymetrix Rice Genome Array, and total number of samples in this series is 26.

first: Masahiro

last: Fujita

first: Youko

last: Horiuchi

first: Yayoi

last: Ueda

first: Yoko

last: Mizuta

first: Takahiko

last: Kubo

first: Kentaro

last: Yano

first: Shinichiro

last: Yamaki

first: Katsutoshi

last: Tsuda

first: Mitsuru

last: Niihama

first: Hirotaka

last: Kato

first: Shunsuke

last: Kikuchi

first: Takako

last: Mochizuki

first: Nobuhiro

last: Tsutsumi


title: Amplification in alveolar rhabdomyosarcoma

status: Public on Oct 16 2010

city: Philadelphia

first: Frederic

last: Barr

state: PA

address: 422 Curie Blvd

institute: University of Pennsylvania

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

summary: Genomic and clinical analyses of major amplification events in alveolar rhabdomyosarcoma

overall_design: Affymetrix SNP 50K XbaI chips were used to anaylyze 57 alveolar rhabdomyosarcoma samples and selected cases were further analyzed using Affymetrix SNP 250K StyI chips

middle: G

first: Fenghai

last: Duan

first: Lynette

middle: M

last: Smith

first: Donna

last: Gustafson

first: Mandy

last: Pitts

first: Sue

last: Hammond

first: Julie

last: Gastier-Foster


title: Transcriptomic shifts in rice roots in response to Cr (VI) stress

city: Lucknow

first: Debasis

last: Chakrabarty

address: Rana Pratap Marg

institute: NBRI

summary: Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice.

overall_design: The rice variety IR-64 was germinated and allowed to grow for 5 d at 37 oC and then transferred to Hewitt solution for growth. After 10 d of growth, seedlings of uniform size and growth were treated with 100 µM of Cr (VI), As (V), Cd, and Pb under standard physiological conditions of 16 h light (115 μmol m−2 s−1) and 8 h dark photoperiod at 25 ± 2°C for 24 h. Total RNA was extracted from the treated rice roots and microarray was performed using one-cycle target labeling and control reagents (Affymetrix platform).

first: Sonali

last: Dubey

first: Prashant

last: Misra

first: Sanjay

last: Dwivedi

first: Sandipan

last: Chatterjee

first: Sumit

middle: K

last: Bag

first: Shrikant

last: Mantri

first: Mehar

middle: H

last: Asif

first: Arti

last: Rai

first: Smita

last: Kumar

first: Manju

last: Shri

first: Preeti

last: Tripathi

first: Rudra

first: Prabodh

last: Trivedi

first: Rakesh

last: Tuli


title: Expression data from field droughted rice plants

status: Public on Sep 09 2010

city: Aberdeen

first: Gareth

last: Norton

address: Crucikshank building

country: United Kingdom

institute: University of Aberdeen

summary:
This study aims to provide a transcriptomics dataset for field grown rice plants subjected to mild drought concentrating on the two parents of a mapping population, Bala and Azucena. Plants were grown in 1.2 m2 plots under flooded conditions in Wuhan, China being sown on 2nd June 2007.  Starting at 59 days after sowing, drought was imposed by withholding water, while a set of control plots had continued flooding conditions. The drought was imposed for 24 days during which time a small amount of water was added on 3 occasions to raise soil moisture to 30% by volume.  After 24 days the second youngest fully expanded leaf was taken and gene expression analysis performed.
We used microarrays to detail the global programme of gene expression underlying drought in rice plants with the aim of using the data to identify candidate genes for drought avoidance QTLs detected within the a rice mapping population.

overall_design: Two rice cultivars, Bala and Azucena, were grown in 1.2 m2 plots under flooded conditions in Wuhan, China being sown on 2nd June 2007.  Starting at 59 days after sowing, drought was imposed by withholding water, while a set of control plots had continued flooding conditions. At 2 pm on the 83rd day after sowing (after 24 days of drought)  the second youngest fully expanded leaf was taken off three plants in two plots per block, the leaves had the top and bottom 4 cm removed and the central portion of the leaf was placed in a bag and then into liquid N2. For the controls there was only one plot of the genotypes per block. There was one bag for each block and three replicate blocks. A total of 6 droughted leaf samples (3 Bala and 3 Azucena) and six control leaf samples (3 Bala and 3 Azucena) were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Adam

last: Price

first: Hamlyn

last: Jones

first: Shaoying

last: Huang

first: Lizhong

last: Xiong


title: Rice expression atlas (4): Vegetative tissues

first: Nori

last: Kurata

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

overall_design:
Regenerating calli on agar plate, young leaves and roots grown in a green house, shoots grown in growth chamber were collected as references of reproductive samples.
Three or four biological replicates at each stage were analyzed with Affymetrix Rice Genome Array, and total number of samples in this series is 25.

first: Masahiro

last: Fujita

first: Youko

last: Horiuchi

first: Yayoi

last: Ueda

first: Yoko

last: Mizuta

first: Takahiko

last: Kubo

first: Kentaro

last: Yano

first: Shinichiro

last: Yamaki

first: Katsutoshi

last: Tsuda

first: Mitsuru

last: Niihama

first: Hirotaka

last: Kato

first: Shunsuke

last: Kikuchi

first: Takako

last: Mochizuki

first: Nobuhiro

last: Tsutsumi


title: Rice expression atlas (2): Pollination - Fertilization

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, time course

overall_design:
Pollinating pistils were collected according to time after pollination. Unpollinatted pistils and pistils 5 min after pollination were separated into stigmas and ovaries.
Two or three biological replicates at each stage were analyzed with Affymetrix Rice Genome Array, and total number of samples in this series is 20.
Unpollinated samples were references in this series.


title: Rice expression atlas: Plant reproductive process

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.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Rice expression atlas (3): Early embryogenesis

overall_design:
0-4 DAP embryosacs were collected, and dissected into bottom 1/4 part (contains embryo) and remaining top 3/4 part (mainly endosperm).
Two or three biological replicates for each tissue-stage were analyzed with Affymetrix Rice Genome Array, and total number of samples in this series is 27.
Unpollinated embryo and ovary samples were references in this series.


title: affy_xoo_rice-Transcriptomics-based identification of Xoo strain BAI3 Talc targets in rice

first: sandrine

last: balzergue

summary:
affy_xoo_rice - affy_xoo_rice - The Bacterial Leaf Blight disease of rice is due to Xanthomonas oryzae pv. oryzae. As for many pathogenic bacteria, it relies on a type 3 secretion system that is devoted to the injection of type 3 effectors into the eukaryotic host cell. These proteins are meant to suppress host basal defense responses and/or mimic some host regulatory function promoting bacterial survey in the plant. We are interested in the functional analysis of a subgroup of Xoo T3Es, that are specialized in host cell transcriptome remodelling. These effectors, therefore called TAL for Transcription Activator-Like proteins (also named AvrBs3/PthA-like), are often key virulence factors essential to Xoo pathogenicity such as the effector protein Talc of african Xoo strain BAI3. Our goal is to understand its function during disease development, by identifying rice host genes that are being directly up- or down-regulated by Talc. To that end, we aim at performing Affymetrix transcriptomic analysis, comparing leaf samples of a susceptible rice line inoculated with Xoo to leaves challenged with a Talc-deficient mutant and water-treated leaves. Highly induced genes are likely to be Talc primary targets and therefore potentially good susceptibility gene candidates.-The goal of the experiment is to identify the rice genes up- or down-regulated by the type III effector Talc from Xoo African strain BAI3, upon the inoculation of susceptible rice leaves 24 hours post-infection. To that end, the experimental design includes the inoculation of Nipponbare rice leaves with the virulent Xoo strain BAI3, that will be compared to Nipponbare rice leaves inoculated with a talc K.O. mutant strain and water.

Keywords: wt vs virulence mutant

overall_design: 9 arrays - rice

first: Julio

last: Saez-Vasquez

first: Sandrine

last: Balzergue

first: Boris

last: Szurek

first: Marie-Laure

last: Martin-Magniette


title: SNP data of MPD/MPN samples

status: Public on Apr 29 2010

city: Tokyo

first: Motohiro

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

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

summary:
Philadelphia-chromosome negative myeloproliferative neoplasms (MPNs) including polycythemia vera, essential thrombocythemia and primary myelofibrosis show an inherent tendency for transformation into leukemia (MPN-blast phase), which is hypothesized to be accompanied by acquisition of additional genomic lesions. We, therefore, examined chromosomal abnormalities by high-resolution single-nucleotide polymorphism (SNP) array in 88 MPN patients, as well as 71 cases with MPN-blast phase, and correlated these findings with their clinical parameters. Frequent genomic alterations were found in MPN after leukemic transformation with up to 3-fold more  genomic changes per sample compared to samples in chronic phase (p<0.001). We identified commonly altered regions involved in disease progression including established targets (ETV6, TP53 and RUNX1), as well as new candidate genes on 7q, 16q, 19p and 21q. Moreover, trisomy 8 or amplification of 8q24 (MYC) was almost exclusively detected in JAK2V617F(-) cases with MPN-blast phase. Remarkably, copy-number neutral-loss of heterozygosity (CNN-LOH) on either 7q or 9p including homozygous JAK2V617F was related to decreased survival after leukemic transformation (p=0.01 and p=0.016, respectively). Our high density SNP-array analysis of MPN genomes in the chronic compared to leukemic stage identified novel target genes and provided prognostic insights associated with the evolution to leukemia.

Keywords: SNP-chip

overall_design: To identify oncogenic lesions in MPD, we performed a genome-wide analysis of primary MPD samples using high-density SNP arrays (Affymetrix GeneChip).

first: Nils

last: Thoennissen

first: Utz

last: Krug

first: Dhong

last: Lee

first: Norihiko

last: Kawamata

first: Gabriela

middle: B

last: Iwanski

first: Terra

last: Lasho

first: Tamara

last: Weiss

first: Daniel

last: Nowak

first: Maya

last: Koren-Michiwitz

first: Masashi

last: Sanada

first: Lee-Yung

last: Shih

first: Arnon

last: Nagler

first: Sophie

last: Raynaud

first: Carsten

last: Muller-Tidow

first: Ruben

last: Mesa

first: Torsten

last: Haferlach

first: D

last: Gilliland

first: Ayalew

last: Tefferi

first: Seishi

last: Ogawa

first: H

middle: P

last: Koeffler


title: Rice leaf transcriptome from 6 week old plants

status: Public on Jul 08 2010

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

summary: Three biological replicates from the leaves of rice genotype Kitaake were obtained for transcriptome analyses. This is part of a study comparing expression and protein levels.

overall_design: Three replicates from plants growing at the same time in greenhouse conditions

first: Pamela

last: Ronald


title: Expression data from rice seedlings of wild type and the CHR729 mutant

status: Public on Nov 04 2010

city: paris

first: yongfeng

last: hu

address: univercite paris-sud Bat 630

institute: IBP

summary: In order to study the function of CHR729 in rice, the T-DNA insertion mutant of CHR729 was obtained and analysed.

overall_design: Total RNAs were extracted from 11-day-old seedlings of both wild type (Hwayoung) and CHR729 mutant plants. Affymetrix GeneChip® Rice Genome Array hybridization was performed with three biological replicates. Data was analyzed with SAM Excel add-in and in-house perl scripts. Results showed that 254 genes are up-regulated, and 345 genes are down-regulated (with q – value at 5%).

first: Y

middle: F

last: Hu

middle: N

last: Liu

middle: X

last: Zhou


title: Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii

status: Public on May 15 2010

city: Straubing

first: Jochen

last: Schmid

address: Schulgasse 16

department: Chair of Chemistry of Biogenic Resources

country: Germany

institute: Technische Universität München

summary:
Two S. rolfsii transcriptomes obtained from scleroglucan-producing and scleroglucan-nonproducing conditions were pooled and sequenced using the 454 pyrosequencing technique yielding ~350,000 reads. These could be assembled into 21,937 contigs and 171,833 singletons, for which 6,951 had significant matches in public protein data bases.
Sequence data were used to obtain first insights into the genomics of scleroglucan and oxalate production and to predict putative proteins involved in the synthesis of both metabolites. Using comparative transcriptomics, namely Agilent microarray hybridization and suppression subtractive hybridization, we identified ~ 800 unigenes which are differently expressed under scleroglucan-producing and non-producing conditions.

overall_design:
Tailor-made microarrays (44K multiplex chip, Agilent) were designed by imaGenes (Berlin, Germany) using an in-house developed method for empirical selection of best performing probes for each gene (Pre Selection Strategy). Briefly, up to ten probes were designed for each of the 454 unigenes (60 bp long oligomers). The 244K Agilent test array was hybridized with pooled Cy3-labeled cRNAs gained form EPSmax13 and EPSmin17 cultures and (in average) two of the best performing oligos were selected for each unigene.   For comparative expression profiling, total RNA was isolated from S. rolfsii, cultured for 37 h in EPSmax13 (biological triplicate) and EPSmin17 media (biological triplicate). RNA quality control, synthesis of Cy3-labeled cRNA including cRNA purification and cRNA quality control, microarray hybridization, scanning and data extraction (Agilent´s feature extraction software) were performed by imaGenes GmbH. Expression data were analyzed by imaGenes GmbH using an in-house developed data analysis pipeline. After quantile normalization, genes were defined as differentially expressed if their expression levels varied at least 2 fold in EPSmax13 samples compared to EPSmin17 samples and if the difference was statistically significant (Student’s t-test, P-value cut-off of 0.05).
454 pyrosequencing cDNA study data was uploaded at SRA and assigned accession number SRP002142.

first: Dirk

last: Müller-Hagen

first: Thomas

last: Bekel

first: Laura

last: Funk

first: Ulf

last: Stahl

first: Volker

last: Sieber

first: Vera

last: Meyer


title: Transcription profiling of parental lines and bulked salt sensitive and salt tolerant RILs derived from 2 rice varieties

status: Public on Apr 20 2010

city: NEW DELHI

first: Awadhesh

last: Pandit

state: DELHI

address: LBS BUILDING

institute: NRC ON PLANT BIOTECHNOLOGY

summary: The aim of this study was to minimize the number of candidate genes responsible for salt tolerance between a pair of rice varieties (CSR27 and MI48) with contrasting level of salt tolerance by bulked segregant analysis of their recombinant inbred lines. Microarray analysis of RNA extracted from the tolerant and susceptible parents without and with stress showed 798 and 2407 differentially expressed genes, respectively.  The number of differentially expressed genes was drastically reduced to 70 and 30,  by pooling the RNAs from ten extreme tolerant and ten extreme susceptible RILs due to normalization of irrelevant differentially expressed genes between the parents.

overall_design: RNA from CSR27, MI48, tolerant bulk and susceptible bulk grown under control and salt stress conditions were analysed in two different biological replications  (A and B) making total sixteen samples

first: Subhasisa

last: Bal

first: Raj

last: Guatum

first: Vandan

last: Rai

first: Rakesh

last: Singh

first: Prakesh

last: Sharma

first: Ashok

first: Kishor

last: Gaikwad

first: Tilk

middle: R

first: Trilochan

last: Mohapatra

first: Nagendra


title: Expression data from rice genotypes FL478 and IR29

status: Public on Jul 07 2010

first: Harkamal

last: Walia

summary:
Salt Stress response of salt-tolerant genotype FL478 compared to IR29
Rice GeneChip was used to find differential expression between two rice genotypes under control and salt stress conditions

Keywords: genotype and treatment comparison

overall_design: Roots (tips) tissue was used for hybridization to GeneChips

first: Timothy

last: Close


title: Genome-wide gene expression of rice cultivar Gui-630 (Indica) X Taiwanjing (Japonica) and mutant lemmata (lem) panicle

status: Public on Mar 12 2010

city: Beijing

first: Wenying

last: Xu

address: Datun Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences

summary:
The lem mutant was discovered in a doubled haploid (DH) line derived from the F1 of Gui-630 (Indica)xTaiwanjing (Japonica) by anther culture. The lem mutant did not affect other traits but caused all other floral organs (including palea, lodicule, stamen and carpel) to homeotically transform into lemma or lemma-like structures and caused floral meristem to be indeterminate, thus resulting in the mutant floret consisting of whorls of lemma and lemma-like organs. To identify the global gene expression changes mediated by LEM, we used 57K Affymetrix rice whole genome array to investigate the differences of genome-wide transcriptome between the young panicles of mutant lem versus WT samples during flower development stage.

Keywords: rice (Oryza sativa L.),wild-type and lemmata mutant

overall_design: We generate gene expression profiles of rice cultivar Gui-630 (indica)x Taiwanjing (japonica) and mutant lemmata by using 57K Affymetrix rice whole genome array.

first: Zhuo

last: Xing

first: Yuanlin

last: Duan

first: Yongbiao

last: Xue

first: Weiren

last: Wu


title: SNP chip data of EWS

status: Public on Apr 01 2010

first: Motohiro

last: Kato

summary:
Ewing sarcoma is one of the solid tumor that developed in children. We performed SNP-chip analysis against 27 specimens of Ewing sarcoma using Affymetrix GeneChip and CNAG/AsCNAR software. Our study revealed the detailed profile of copy number alterations in Ewing sarcoma.

Keywords: SNP-chip

overall_design: To identify oncogenic lesions in Ewing sarcoma, we performed a genome-wide analysis of Ewing sarcoma samples using high-density SNP arrays (Affymetrix GeneChip).

first: Junko

last: Takita

first: Yuyan

last: Chen

first: Kentaroh

last: Ohki

first: Masashi

last: Sanada

first: Takashi

last: Igarashi

first: Yasuhide

last: Hayashi

first: Seishi

last: Ogawa

first: Riki

last: Nishimura


title: Microarray data from aerial tissue of submergence tolerant M202(Sub1) and intolerant M202

status: Public on Feb 04 2010

city: Riverside

first: Takeshi

last: Fukao

address: Department of Botany and Plant Sciences

institute: University of California, Riverside

summary: An ERF transcription factor, Submergence-1A (Sub1A), dramatically enhances the tolerance to prolonged submergence in rice. For instance, rice accessions which lack Sub1A (e.g. M202) die within 7-10 d of complete submergence. By contrast, genotypes which posses Sub1A (e.g. M202(Sub1)) can endure submergence stress for 14 d. In this study, the two near isogenic lines with and without Sub1A were subjected to microarray analysis using Affymetrix Gene Chip technology. This analysis provided beneficial information to elucidate general response to submergence stress and to estimate Sub1A-dependent defense response to the stress at mRNA accumulation level.

overall_design: Aerial tissue of 14-d-old plants which were submerged for 24 h were subjected to RNA extraction and hybridization on Affymetrix microarrays. Non-submerged plants were used as control. Two independent biological replicates were analyzed for each treatment/genotype.

first: Julia

last: Bailey-Serres


title: Whole-Genome Analysis of SSB Larvae Infestation Regulated Rice Genes

status: Public on Mar 18 2011

city: Hangzhou

first: Guoxin

last: zhou

state: Zhejiang

address: Kaixuan Road 268

institute: Zhejiang University, Institute of Insect Science

summary: Rice, the world’s most important food crop, is attacked by multiple herbivores and pathogens.the rice striped stem borer (SSB) Chilo suppressalis is one of another most important rice insect pests. Here, we use Affymetrix Whole-Genome rice arrays to detect SSB infestation responsive genes.

overall_design: RNA samples from five damaged stems of SSB-challenged 24 h rice plants or five stems from unchallenged plants (for control samples) were used to array analysis. Two replicate biological experiments of SSB treatment rice arrays and one control samples array were peformed.

first: Yonggen

last: Lou

last: Zhou


title: Affymetrix SNP array data for NSCLC and CRC

status: Public on Aug 06 2010

city: Abbott Park

first: Xin

last: Lu

state: IL

address: 100 Abbott Park Rd

department: Cancer Research

institute: Abbott Laboratories

summary:
Cancer is a heterogeneous disease caused by genomic aberrations and characterized by significant variability in clinical outcome and response to therapies. Several subtypes of common cancer types have been identified based on alterations of individual cancer genes, such as HER2, EGFR, and others. However, cancer is a complex disease driven by the interaction of multiple genes, so the copy number status of individual genes is not sufficient to define cancer subtypes and predict the response to treatments. A classification based on genome-wide copy number patterns would be better suited for this purpose.
To develop a more comprehensive cancer taxonomy based on genome-wide patterns of copy number abnormalities, we designed an unsupervised gNMF-based classification algorithm that identifies genomic subgroups of tumors. The algorithm was subjected to a stability test and validated by demonstrating clinical differences between samples assigned to different clusters.
Our algorithm demonstrated better performance in the stability test when compared with other clustering methods.  Most importantly, it yielded better separation between groups of samples with distinct clinical outcomes, implying that it classifies samples into clinically relevant subgroups. We propose using this methodology to identify unknown subtypes of cancers and to assemble panels of pre-clinical testing models that would represent different subtypes of cancers.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions.
Copy number analysis of Affymetrix 100K SNP arrays was performed for 40 non-small cell lung carcinoma cell lines, 205 non-small cell lung carcinoma primary tumors, 35 colorectal cancer cell lines, and 101 colorectal cancer primary tumors.

first: Ke

last: Zhang

first: Charles

last: VanSant

first: John

last: Coon

first: Dimitri

last: Semizarov


title: A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression array: Transcript and Genome Hybridizations

status: Public on Jun 01 2010

first: Nori

last: Kurata

type:
Expression profiling by array
Genome variation profiling by array

summary: The publicly available genome sequence information of two rice strains, japonica cultivar Nipponbare and indica cultivar 93-11, opens a great opportunity for investigation of performances DNA genotyping by high-density oligonucleotide arrays. Here, we compare single feature polymorphism (SFP) detection performances between whole genome hybridization and transcript hybridization using Affymetrix Rice Expression Array and the two rice cultivars.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: Total RNA  from 3-4 week shoots and genomic DNA both Nipponbare and 93-11 were analyzed.

first: Youko

last: Horiuchi

first: Yoshiaki

last: Harushima


title: Whole genome transcriptome profiling of Pusa 1266 and Pusa Basmati 1 in panicle primordia stage

city: New Delhi

first: Rupesh

middle: Kailasrao

last: Deshmukh

address: Libraryavenue, PUSA

department: Rice Genome Laboratory

institute: National Research Center on Plant Biotechnology

summary: The aim of this study was to identify candidate genes responsible for grain number per panicle between a pair of rice varieties (Pusa 1266 and Pusa Basmati 1) by combining QTL analysis with expression analysis.   Microarray analysis of RNA extracted from the panicle primordia showed 2741 differentially expressed genes.  The differentially expressed genes were shortened to 18 on the basis of their occurance in the QTL region (responsible for grain number regulation) detected in RIL population derived from Pusa 1266 and Pusa Basmati 1.

overall_design: RNA from the stage '0' panicle primordia of Pusa 1266 and Pusa Basmati 1 were analysed in two different biological replications  (A and B) making total four samples

first: Abhinay

last: Singh

first: Neha

last: Jain

first: Ashok

first: Kishor

last: Gaikwad

first: Tilk

last: Sharma

first: Trilochan

last: Mohapatra

first: Nagendra


title: Expanded MLST genotyping and comparative genomic hybridization of Campylobacter coli isolates from multiple hosts

status: Public on Feb 02 2010

city: Ithaca

first: Michael

middle: J

last: Stanhope

state: NY

address: Schurman Hall

department: Population Medicine and Diagnostic Sciences

institute: Cornell University

summary:
Although the majority of previous work on campylobacteriosis has centered on the species Campylobacter jejuni, Campylobacter coli, the sister group to C. jejuni, is also a significant problem, but remains a much less studied organism. The purpose of this study was to develop and apply an expanded 16 locus MLST genotyping scheme to a large collection of C. coli isolates sampled from a wide range of host species, and to complete microarray comparative genomic hybridizations for these same strains, in order to: (1) determine whether host specific clones, genotypes, or clonal complexes are evident and (2) evaluate whether there are particular genes comprising the dispensable portion of the C. coli genome that are more commonly associated with certain host species. Genotyping and ClonalFrame analyses of the expanded MLST data suggest that (1) host preferred groups have tended to evolve in the diversification of C. coli, (2) this has happened repeatedly, at different times, throughout the evolutionary history of the species, and (3) recombination has played varying roles in the diversification of the different groups.  Concomitant with the information on evolutionary history derived from the MLST data, the microarray data suggests that a combination of common ancestry in some cases and lateral gene transfer in others are behind a tendency for sets of genes to be common to isolates derived from particular hosts.

Keywords: comparative genomic hybridization

overall_design: Combimatrix CustomArray™ 4X2K was used in this study.  This array is divided into 4 sectors, each of which contains 2,240 in situ synthesized oligonucleotide probes (spots) with the same probe design and layout.   Based on the sequence of Campylobacter coli strain RM2228, oligonucleotide probes were designed to have a similar annealing temperature of 56ºC and a length 35-40 bp.  Two separate designs were used in this study; both included 100 control probes (20 negative controls with sequences from plant and phage, each with 5 replicate spots) as well as loci from the RM2228 genome. Because of the strict criteria for probe design, not all ORFs could be covered in this analysis. The first design included 1942 of the 1967 protein coding genes described in the unfinished sequence of C. coli strain RM2228.  The second-generation design was based on genes that were not clearly present (loci with low intensity or no hybridization for at least one strain) in the hybridization results involving the first design. The second design included additional two or five probes, separated from one another in order to span the entire gene, for these 615 ambiguous loci, synthesized in situ to occupy the 2,240 independent microarray spots.   Replicate microarrays were hybridized for every 65 strains tested in this study.

first: Ping

last: Lang

first: Tristan

last: Lefebure

first: Wei

last: Wang

first: Paulina

last: Pavinski Bitar

first: Richard

last: Meinersmann

first: Katherine

last: Kaya


title: FACS-sorted Pancreatic Adenocarcinoma for Molecular Profiling

status: Public on Feb 18 2010

city: South San Francisco

first: Peter

last: Haverty

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
Frozen, whole tissue was dissociated and sorted into to tumor and stromal fractions via FACS

Keywords: Mapping Array

overall_design: Profiling of tumor and stromal fractions from whole tissue

first: Zach

last: Boyd

first: Rob

last: Soriano

first: David

last: Eberhard

first: Rajiv

last: Raja

first: Stephanie

last: Johnson

first: Mark

last: Lackner


title: Transgenic rice line carrying the maize resistance gene Rxo1 to Xanthomonas oryzae pv. oryzicola

status: Public on Dec 11 2009

first: Meirong

last: Xu

state: Beijing

address: 12 South Zhong-Guan-Cun St.

department: Institute of Crop Sciences

institute: Chinese academy of agricultural sciences

summary:
Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola
Non-host resistance in rice to its bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), mediated by a maize NBS-LRR type R gene, Rxo1 shows a typical hypersensitive reaction (HR) phenotype, but the molecular mechanism(s) underlying this type of non-host resistance remain largely unknown. Results A microarray experiment was performed to reveal the molecular mechanisms underlying HR of rice to Xoc mediated by Rxo1 using a pair of transgenic and non-transgenic rice lines. Our results indicated that Rxo1 appeared to function in the very early step of the interaction between rice and Xoc, and could specifically activate large numbers of genes involved in signaling pathways leading to HR and some basal defensive pathways such as SA and ET pathways. In the former case, Rxo1 appeared to differ from the typical host R genes in that it could lead to HR without activating NDR1. In the latter cases, Rxo1 was able to induce a unique group of WRKY TF genes and a large set of genes encoding PPR and RRM proteins that share the same G-box in their promoter regions with possible functions in post-transcriptional regulation.
In conclusion, Rxo1, like most host R genes, was able to trigger HR against Xoc in the heterologous rice plants by activating multiple defensive pathways related to HR, providing useful information on the evolution of plant resistance genes. Maize non-host resistance gene Rxo1 could trigger the pathogen-specific HR in heterologous rice, and ultimately leading to a localized programmed cell death which exhibits the characteristics consistent with those mediated by host resistance genes, but a number of genes encoding pentatricopeptide repeat and RNA recognition motif protein were found specifically up-regulated in the Rxo1 mediated disease resistance. These results add to our understanding the evolution of plant resistance genes.

overall_design: All inoculated flag leaves from three plants of 9804-Rxo1 and 9804 were collected two days post-inoculation (dpi), and the flag leaves from three non-inoculated check plants of 9804-Rxo1 and 9804 were also sampled at the same time point as control. The flag leaves from non-inoculated check plants of 9804 were sampled at the same time point as control: 9804-Rxo1 (3-replications), XOC - time: 2 dpi(3-replications); 9804-Rxo1 (3-replications); 9804, XOC - time: 2 dpi(3-replications) 9804. 2 sets of separately normalized data: 9804-Rxo1 and 9804.

first: Yongli

last: Zhou

first: Mingfu

last: Zhao

first: Xuewen

last: Xie

first: Linghua

last: Zhu

first: Binying

last: Fu

first: Zhikang

last: Li


title: Affymetrix SNP array data for pediatric acute myeloid leukemia (AML) samples at diagnosis: Xba SNP array

status: Public on Jan 04 2010

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

summary:
Genome-wide profiling of Copy Number Alterations (CNA) and Loss of Heterozygosity (LOH), gene expression and resequencing of pediatric AML.
This study characterizes the CNA and LOH in a representative cross-section through subtypes of pediatric AML. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples.

overall_design:
111 pediatric AML samples were studied using either Affymetrix 100K + 500K 5.0 SNP arrays, 65 of the samples had paired germ line material.

The supplemental file 'GSE15732_AML_175_SNP_Xba_signal.txt' contains the raw signals generated by dChip without normalization.

The CNA and LOH data can be found in the Supplemental Information of the associated manuscript.

first: Ina

last: Radtke

first: James

last: Downing


title: Affymetrix SNP array data for pediatric acute myeloid leukemia (AML) samples at diagnosis: Hind SNP array

overall_design:
111 pediatric AML samples were studied using either Affymetrix 100K + 500K 5.0 SNP arrays, 65 of the samples had paired germ line material.

The supplemental file 'GSE15714_AML_175_SNP_Hind_signal.txt' contains the raw signals generated by dChip without normalization.

The CNA and LOH data can be found in the Supplemental Information of the associated manuscript.


status: Public on Jan 01 2010

first: Rupesh

last: Deshmukh

summary:
Whole genome transcriptome profiling of bulked RILs with high and low grain number per panicle derived from 2 cultivars at panicle primordia stage

The aim of this study was to identify candidate genes responsible for grain number per panicle by combining QTLs analysis with expression analysis.   Microarray analysis of RNA extracted from the panicle primordia showed 20 differentially expressed genes, respectively.  The differentially expressed genes were shorted to 4 on the basis of their occurance in the QTL region (responcible for grain number regulation) detected in RIL population derived from Pusa 1266 and Pusa Basmati 1.

overall_design: RNA from the stage '0' panicle primordia of 10 RILs with high grain number and 10 with low grain number were bulked and analysed in two different biological replications  (A and B) making total four samples

first: Abhinay

last: Singh

first: Neha

last: Jain

first: R

last: Gacche

first: Ashok

first: Kishor

last: gaikwad

first: Tilk

last: Sharma

first: Trilochan

last: Mohapatra

first: Nagendra


title: Affymetrix SNP array data for Genomic Instability and Myelodysplasia with Monosomy 7

status: Public on Jan 13 2010

city: Heidelberg

first: Sandrine

last: Tchatchou

address: Voßstrasse 9

department: Molecular Biology Labor

institute: Universität Frauenklinik Heidelberg

summary: Gene modified autologous hematopoietic stem cells (HSC) can provide significant clinical  benefits to patients suffering from X-linked chronic granulomatous disease (X-CGD), a rare  inherited immunodeficiency characterized by recurrent, often life threatening bacterial and fungal infections. Here we report on the molecular and cellular events observed in two patients treated by gene therapy in 2004. After the initial resolution of bacterial and fungal infections, both patients exhibited silencing of transgene expression due to methylation of the viral promoter, and myelodysplasia with monosomy 7 as a result of insertional activation of EVI1. One patient died from overwhelming sepsis 27 months after gene therapy, whereas a second patient underwent an allogeneic HSC transplantation. Our data shows that forced overexpression of MDS1/EVI1 or EVI1 in human cells disrupts normal centrosome duplication, linking MDS1/EVI1 activation to the development of genomic instability, monosomy 7 and clonal progression towards myelodysplasia.

overall_design:
Genomic copy number alterations were detected by analyzing the fluorescence signal intensities of each SNP on the GeneChip Human Mapping 100K array st (Affymetrix, Santa Clara, Ca) with the Copy Number Analyzer for Affymetrix GeneChip 100K arrays (CNAT) version 2.0. The log2 ratio of each SNP, the local averaged log2 signal ratio (averaged for 10 SNPs) and the inferred chromosome copy number according to the Hidden Markov Model (HMM) were calculated.
Copy number analysis of Affymetrix 100K SNP arrays was performed for one young adult with the X-linked chronic granulomatous disease (X-CGD)


title: Identification of Acquired Copy Number Alterations and Uniparental Disomies in Cytogenetically Normal AML

status: Public on Dec 01 2009

city: Ulm

first: Jan

last: Kroenke

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine III

institute: University Hospital of Ulm

summary:
Identification of Acquired Copy Number Alterations and Uniparental Disomies in Cytogenetically Normal Acute Myeloid Leukemia Using High-Resolution Single Nucleotide Polymorphism Analysis
Recent advances in genome-wide single nucleotide polymorphism (SNP) analyses have revealed previously unrecognized microdeletions and uniparental disomy (UPD) in a broad spectrum of human cancers. As acute myeloid leukemia (AML) represents a genetically heterogeneous disease, this technology might prove helpful especially for cytogenetically normal AML (CN-AML) cases. Thus, we performed high-resolution SNP analyses in 157 adult cases of CN-AML. Regions of acquired UPD were identified in 12% of cases and most frequently affected chromosomes 6p, 11p, and 13q. Notably, acquired UPD was invariably associated with mutations in NPM1 or CEBPA that impair hematopoietic differentiation (P=0.008), suggesting that UPDs may preferentially target genes that are essential for proliferation and survival of hematopoietic progenitors. Acquired copy number alterations (CNAs) were detected in 49% of cases with losses found in two or more cases affecting e.g. chromosome bands 3p13-p14.1 and 12p13. Furthermore, we identified two cases with a cryptic t(6;11) as well as several non-recurrent aberrations pointing to leukemia relevant regions. With regard to clinical outcome, there appeared to be an association between UPD 11p and UPD 13q cases with overall survival. These data demonstrate the potential of high-resolution SNP analysis for identifying genomic regions of potential pathogenic and clinical relevance in AML.

overall_design: Copy number analysis of Affymetrix 50K and/ or 500K SNP arrays was performed for 157 adult AML samples

first: Lars

last: Bullinger

first: Hartmut

last: Doehner


title: Gene expression in leaf blades of the rice Os-LBD37 overexpressor line RK16331-13

status: Public on Dec 27 2009

city: Yokohama

first: Miyako

last: Kusano

state: Kanagawa

address: 1-7-22, Suehiro, Tsurumi

institute: RIKEN CSRS

summary: The 5th and 6th leaf blades of the rice Os-LBD37 overexpressor line RK16331-13 and the empty vector control line FOX3 were examined. LBD37 belongs to the plant- specific LOB- (Lateral Organ Boundary) domain family proteins first characterized in Arabidopsis. Results point towards an involvement of the rice LBD37 (OsLBD37) ortholog of Arabidopsis in nitrogen metabolism- and senescence- related processes.

overall_design:
Hygromycin- resistant rice Os-LBD37 overexpressor and empty vector control plants were grown in hydroponic culture system. The sampling date of the leaf blades of RK16331-13 LBD37 overexpressor plants and the empty vector control was determined according to the emergence of the 8th leaf blade.
Three independent hybridizations were performed for line RK16331-13 and the empty vector control line.


title: SNP array data for 50 leukemia remission samples

status: Public on Sep 02 2009

first: Charles

last: Mullighan

summary:
250k Sty, 250k Nsp, 250k Hind and 250k Xba Affymetrix SNP arrays for 50 leukemia remission samples used as controls for copy number analysis for GSE9109 and GSE9112.
Keywords: Acute leukemia, BCR-ABL1, chronic myeloid leukemia, copy number analysis, loss-of-heterozygosity, genomics

*** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. ***

overall_design: All assays were performed on DNA extracted from cryopreserved, mononuclear cell preparations of diagnostic peripheral blood or bone marrow samples. All blast crisis samples were flow sorted prior to DNA extraction. SNPcalls were generated using Affymetrix GTYPE. Probe intensity data wasextracted and used for DNA copy number analysis using dChip, akaryotype-guided normalization algorithm (Reference normalization, Mullighan et al Nature 2007;446:758), dChip and circular binarysegmentation (implemented as DNAcopy in R).


title: Transcriptional profiling of Cellulase induced hypersensitive reaction like response in rice

status: Public on Dec 24 2009

city: Hyderabad

first: Ramesh

middle: V.

last: Sonti

state: Andhra Pradesh

address: Uppal Road

department: Plant Microbe Interactions

institute: Centre for cellular and molecular biology (CCMB)

summary:
Cellulase, a Type II secretion system secreted protein of Xanthomonas oryzae pv. oryzae (Xoo; the casual of bacterial leaf blight of rice) is a potent inducer of   rice defense responses such as hypersensitive response like reactions (HR), callose depositions, cell death associated with nuclear fragmentations and impart functional resistance against further Xoo inoculation
In order to understand the molecular events associated with cellulase induced HR in rice, whole genome transcriptional profiling was performed using Affymetrix Rice GeneChips
Keywords: Expression profiling of a hypersensitive reaction like response

overall_design: Leaves of 20 days old green house grown susceptible rice cultivar (Taichung Native-1; TN-1) were infiltrated with either 30-40μl of purified Xoo cellulase (5μg/ml) or with buffer (10mM potassium phosphate buffer pH 6.0) alone (as described in Jha et al. 2007; MPMI vol 20, pp 31-40). The plants were shifted to a growth chamber (28oC; 80% relative humidity; 12/12h light/dark cycle) 48 hours before the treatment. 20-30 leaf pieces covering the infiltrated zone from each of the treatments were harvested 12 h after infiltration. Total RNA isolated from the pooled samples was subjected for expression analysis using Affymetrix GeneChip System. The experiment was repeated with three different biological replicates using RNA isolated from three batches of rice leaves treated with the freshly purified Xoo cellulase and the buffer

first: Gopaljee

last: Jha

first: Hitendra

last: Patel

first: Palaparthi

last: Ramesh

middle: V


title: Temporal gene expression analyisis from rice root (cv. Nipponbare) infected with Magnaporthe oryzae strain Guy11

status: Public on Oct 02 2009

city: Lausanne

first: Sylvain

last: Marcel

state: VD

address: Campus Dorigny

country: Switzerland

institute: University of Lausanne

summary: Magnaporthe oryzae causes rice blast, the most devastating foliar fungal disease of cultivated rice. During disease development the fungus simultaneously maintains both biotrophic and necrotrophic growth corresponding to a hemi-biotrophic life style. The ability of M. oryzae to also colonize roots and subsequently develop blast symptoms on aerial tissue has been recognized. The fungal root infection strategy and the respective host responses are currently unknown. Global temporal expression analysis suggested a purely biotrophic infection process reflected by the rapid induction of defense response-associated genes at the early stage of root invasion and subsequent repression coinciding with the onset of intracellular fungal growth. The same group of down-regulated defense genes was increasingly induced upon leaf infection by M. oryzae where symptom development occurs shortly post tissue penetration. Our molecular analysis therefore demonstrates the existence of fundamentally different tissue-specific fungal infection strategies and provides the basis for enhancing our understanding of the pathogen life style.

overall_design: We investigated global transcriptome response overtime of Mock- and M. oryzae inoculated rice root tissue in vitro. Two independant replicates were perfomed for each treatments and samples were collected at 2, 4 and 6 days post-inoculation.

first: Ruairidh

last: Sawers

first: Edward

last: Oakeley

first: Herbert

last: Angliker

first: Uta

last: Paszkowski


title: Somatic mutations in p85α promote tumorigenesis through p110α activation

status: Public on Oct 01 2009

city: San Diego

first: Zhengyan

last: Kan

address: 10770 Science Center Drive

department: Computational Biology, Oncology Research & Development

institute: Pfizer

summary: Frequent mutations in the regulatory p85a subunit (PIK3R1 gene) were identified in colon cancer and shown to promote cell survival, Akt activation, anchorage independent cell growth and oncogenesis. A number of tumor samples including colon, breast, NSCLC and gastric were also profiled for co-occurrence of chromosomal copy number changes including gene amplifications in PI3K pathway on Affymterix 100K SNP arrays.

overall_design: Analysis of copy number changes in several different tumor types

first: Somasekar

last: Seshagiri

first: Zora

last: Modrusan

first: Bijay

last: Jaiswal


title: SNP array data for 304 pediatric and adult acute lymphoblastic leukemia cases

summary:
Copy number and LOH analysis was performed for 304 casesof B-progenitor and T-lineage acute lymphoblastic leukemia. All caseswere genotyped with Affymetrix 250k Sty and Nsp arrays. 252 cases werealso genotyped with Hind and Xba arrays.
Keywords: Acute leukemia, BCR-ABL1, copy number analysis, loss-of-heterozygosity, genomics

*** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. ***

overall_design: All assays were performed on DNA extracted fromcryopreserved, mononuclear cell preparations of diagnostic peripheralblood or bone marrow samples. Samples with less than 80% blasts wereflow sorted prior to DNA extraction. SNP calls were generated usingAffymetrix GTYPE. Probe intensity data was extracted and used for DNAcopy number analysis using dChip, a karyotype-guided normalizationalgorithm (Reference normalization, Mullighan et al Nature2007;446:758), dChip and circular binary segmentation (implemented asDNAcopy in R). Copy number inferences were made using a set of 50 acuteleukemia remission samples (GSE9111).

first: James

last: Downing


title: Affymetrix SNP array data for acute lymphoblastic leukemia samples

summary:
BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. The Philadelphia chromosome, encoding BCR-ABL1, is the defining lesion of chronic myelogenous leukemia (CML) and a subset of acute lymphoblastic leukemia (ALL) cases. To define oncogenic lesions that cooperate with BCR-ABL1 to induce ALL, we performed genome-wide analysis of leukemic samples from 23 CML cases and 304 ALL cases, including 43 BCR-ABL1 B-ALL cases. IKZF1 (encoding the transcription factor Ikaros) was deleted in 83.7% of BCR-ABL1 B-ALL cases, but not in chronic phase CML. Deletion of IKZF1 was also identified as an acquired lesion in lymphoid blast crisis of CML. The IKZF1 deletions resulted in haploinsufficiency, expression of a dominant negative Ikaros isoform or the complete loss of Ikaros expression. Sequencing of IKZF1 deletion breakpoints suggested that aberrant V(D)J recombination is responsible for the deletions. These findings suggest that genetic lesions resulting in the loss of Ikaros function are a key event in the development of BCR-ABL1 ALL.

*** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. ***

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Affymetrix SNP arrays were performed according to the maufacturers directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples.
Copy number analysis of Affymetrix 100K and 500K SNP arrays was performed for 304 pediatric and adult ALL samples, 23 chronic myeloid leukemia samples, and 36 ALL cell lines. There are also 50 samples from leukemia in remission, which were used as references for copy number inference.