title: Activating of jasmonic acid pathway through depletion of rice hydroperoxide lyase OsHPL3 revealed a crosstalk between HPL- and AOS-branch oxylipin pathways in rice

status: Public on Aug 21 2013

city: Beijing,

first: Xiaoqiang

last: Liu

department: Chinese academy of sciences

institute: the institute of genetics and developmental biology

summary: The allene oxide synthase (AOS) branch and the hydroperoxide lyase (HPL) branch of the oxylipin pathway function in plant responses to diverse stresses and have potential cross-talks between each other in the biosynthesis and signaling regulation, but there is still an absence of direct evidence and detailed information about this communication. Here, we identified and characterized a jasmonates acid (JA) overproduction mutant, cea62, by screening the Constitutive Expression of AOS gene (cea) from rice T-DNA insertion mutant library. Map-based cloning was used to isolate the target gene as the hydroperoxide lyase OsHPL3 gene. The gene expression, HPL enzyme activity and its resulting products, (E)-2-hexenal, were all depleted in the cea62 mutant, which resulted in dramatic JA overproduction and activation of JA signaling in the mutant. Consistent with the formation of the lesion mimic phenotype and the timing of the induction for some defense responsive genes, the activation of JA biosynthesis and signaling was regulated in a developmental way, just as the way by which OsHPL3 was regulated in the wild type plant. Microarray data showed that the JA-governed defense response was greatly activated in the cea62 mutant plant and the cea62 plant obtained enhanced resistance to the bacterial blight pathogen Xanthomonasoryzaepvoryzae (Xoo) T1 strain. Wounding response was attenuated in the cea62 mutant at an early developmental stage, while it was partially recovered when JA levels were elevated at a later developmental stage in the cea62 mutant. But, the wounding response was not altered at different developmental stages in the wild type plant. These findings suggest that these two branches of the oxylipin pathways crosstalked in the biosynthesis and signaling pathways and cooperated with each other to function in diverse stress responses.

overall_design: We compared the gene expression profile in leaf tissues of the wild-type plant and the cea62 mutant after lesion mimic phenotype appeared two months after sowing. Total RNAs were extracted from leaf blades from the rice (Oryza sativa L.) wild-type Nipponbare plant and from leaf blades of the rice (Oryza sativa L.) cea62 mutant in the Nipponbare (ssp japonica) background at two months after sowing. Three replicates of the cea62 mutant and wild type were performed.

first: Feng

first: Jiuyou

last: Tang

first: Weihong

first: Fengxia

first: Guodong

first: Jinfang

last: Chu

first: Cunyu

last: Yan

first: Taoqing

first: Chengcai

first: Chuanyou


title: Chromothripsis in AML

status: Public on Aug 04 2013

city: Fitzroy

first: Ruth

middle: N

last: MacKinnon

state: Vic

address: PO Box 2900

department: Victorian Cancer Cytogenetics Service

country: Australia

institute: St Vincent's Hospital (Melbourne)

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

summary:
This dataset contains data from two acute myeloid leukaemia (AML) specimens processed with the Illumina CytoSNP-12 SNP array platform.
SNP array data showed evidence of chromothripsis in these two specimens. Each deletion in the mosaic specimen was present in the same proportion of cells, which supports the view that the many breaks occur as a single event. Complementary FISH studies highlighted the inclusion of centromeres from different chromosomes during the formation of the new chromosomes.

overall_design: Residual bone marrow specimens were chosen from patients who were determined to have a complex karyotype which included abnormalities of chromosomes 5 and 17, by routine cytogenetic examination.


title: ivt-Transcriptomic study of rice seed ageing

status: Public on Sep 01 2013

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

summary: affy_rice_2012_01 - ivt - One of the key questions for future agriculture will be to save agronomical relevant biodiversity. To do so, it is important to select the best crop cultivars that will germinate efficiently (good seed vigor) and for a long period of time (good seed longevity). Surprisingly, while mankind rely heavily on cereals, very few studies have identified genes positively related to cereal seed vigor and longevity. To close this scientific gap, we aimed to identify genes positively involved in rice seed vigor and longevity. We thus used a “controlled deterioration treatment (Tesnier et al., 2002) to mimic natural seed ageing. Seeds are first equilibrated at 25°C and 85% relative hygrometry during three days. Then, during 15 days, three different batch of seeds are either (i) kept at 25°C and 85% RH (control seeds), (ii) placed at 40°C and 85% RH (loss of seed vigor) or (iii) placed at 45°C and 85% RH (loss of germination capacity). Finally, seeds are equilibrated at 25°C and 32% RH during three days. Using this CDT treatment, we obtained rice seeds with contrasted seed vigor or germination capacity. We extracted the total RNA from the embryos and we analysed their transcriptome using the Affymetrix Rice Genome Array.-We applied a Controlled Deterioration Treatment (CDT) to seeds from the reference rice cultivar Nipponbare. First, all seeds are equilibrated at 25°C and 85% relative hygrometry. Then, depending on the treatment, seeds are placed at 25, 40 or 45°C in 85% relative hygrometry before being finally equilibrated at 25°C and 32% relative hygrometry. The germination of the three seed batches was measured during five days with one measure every 8h. Seeds placed at 25°C during the whole experiment were similar to control seeds kept in the fridge and germinated at nearly 100% in 48h. Seeds placed at 40°C during 15 days germinate at 74% but show altered seedling phenotypes (loss of seed vigor). Finally, seeds placed at 45°C do not germinate.

overall_design: 12 arrays - rice; treated vs untreated comparison

first: Stephanie

last: Huguet

first: MARC

last: GALLAND

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Affymetrix SNP array data for acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS)

status: Public on Jul 16 2013

city: Tokyo

first: Ayana

last: Kon

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

department: Cancer Genomics Project

country: Japan

institute: The University of Tokyo

summary:
We recently identified recurrent mutations of cohesin complex in myeloid neoplasms through whole-exome sequencing analysis.
In this study, we performed SNP array analysis to detect abnormal copy number of the cohesin genes.

overall_design: Copy number analysis by Affymetrix 50K or 250K SNP arrays was performed for 93 AML and 70 MDS tumor samples.

first: Masashi

last: Sanada

first: Aiko

last: Sato-Otsubo

first: Kenichi

last: Yoshida

first: Yasunobu

last: Nagata

first: Yusuke

last: Sato

first: Yuichi

last: Shiraishi

last: Okuno

first: H

middle: P

last: Koeffler

first: Lee-Yung

last: Shih

first: Seishi

last: Ogawa


title: Genomic alteration in MRC5-derived induced pluripotent stem (MRC5-iPS) cell line, Tic

status: Public on Jul 23 2013

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

type: Genome variation profiling by genome tiling array

summary: Disease-specific induced pluripotent stem (iPS) cells have been used for a model to analyze pathogenesis of the disease. We generated iPS cells derived from a fibroblastic cell line of ataxia telangiectasia (AT-iPS cells). In analysis of AT-iPS cells, the human wild-type iPS cell line (MRC5-iPS) was generated and cultured in the same conditions as the diseased iPS cell lines. It is an ideal control cell line for the disease and patient-specific iPS cell lines.  Because MRC5-iPS cells exhibited considerable chromosomal abnormalities in vitro, we performed a structural alteration analysis by using a SNP genotyping array for MRC5-iPS cell line, Tic,  at passage 15,  passage 30, and  passage 37.

overall_design: The parental MRC-5 fibroblast cells and MRC-iPS 25 (Tic)  were subjected to Illumina HumanCytoSNP-12 v2.1 BeadChip analysis.

first: Toyoda

last: Masashi

first: Kazuhiro

last: Nakabayashi

first: Kohji

last: Okamura

first: Kenichiro

last: Hata


title: Gene expression data for rice grain (Oryza sativa L.) aroma performed using bulk pools of aromatic and non-aromatic RILs derived from a cross between Pusa 1121 and Pusa 1342

status: Public on Jun 11 2013

city: new delhi

first: vinita

last: pachauri

state: delhi

address: pusa campus

department: rice genome

country: India

institute: NRCPB

summary:
Gene expression profile was studied to complement fine mapping studies. Genes co-located in the previously reported three aroma QTLs viz. qaro3.1, qaro4.1 and qaro8.1 were identified.
Microarrays were used to study gene expression profile to reduce the number of up- and down regulated genes co-located within the reported aroma QTLs. These genes are the most suitable candidates for further validation studies and development of molecular markers to assist in Marker assisted Breeding for the development of new improved fragrant rice varieties.

overall_design: Six extreme aromatic RILs and six extreme non-aromatic RILs were identified on the basis of their sensory aroma scores. The RILs were pooled together to make two different bulk groups: aromatic bulk (VA) and non-aromatic bulk (VN). The two parents, Pusa 1121, the aromatic parent (VPA) and Pusa 1342, the non-aromatic parent (VRN) were also taken as two groups. RNA was isolated from fresh leaves  after about 20-25 days of transplanting seedlings into experimental field, stage at which grain aroma develops. Four biological replicates (1-4) for each group were taken making a total of 16 samples.

first: Vinita

last: Pachauri

first: Vagish

last: Mishra

first: Pragya

first: Nagendra

middle: K

last: Singh


title: Expression data from OsEBS-transgenic rice B10201 and B10301 and control Guichao2

status: Public on May 04 2013

city: Shanghai

first: Xianxin

last: dong

address: 220 Handan Road

department: School of Life Sciences, Fudan University

country: China

institute: State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Science Research

summary:
In rice (Oryza sativa L.), the number of panicles, spikelets per panicle and grain weight are important components of grain yield. These characteristics are controlled by quantitative trait loci (QTLs) and are derived from variation inherent in crops.The identification of different yield related QTLs facilitates an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops.  an understanding of the mechanisms involved in cereal crop yield, and may have utility  in improving grain yield in cereal crops.
In the present study, We cloned and characterized a large-panicle QTL, and confirmed that the newly identified gene OsEBS (enhancing biomass and spikelet number) increased plant height, leaf size and spikelet number per panicle, leading to an average of 37.62% increase in total grain yield per plant.
trait loci (QTLs) and are derived from variation inherent in crops.

last: Dong

first: Xiaojin

last: Luo


title: Genome-wide mRNA profiling for identification of specific body fluid markers

status: Public on Jan 22 2013

city: Daejon

first: Seon-Young

last: Kim

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Genome-wide expression profiling of four kinds of body fluid samples (blood, saliva, semen and vaginal swab). The purpose of the present study was selection of specific mRNA markers for identification of the four body fluids. Results provide important information about gene expression level of each body fluid for forensic science.

overall_design: Total RNAs isolated from four kinds of body fluid samples (blood, saliva, semen and vaginal swab) obtained from Korean volunteers

first: Jeong-Hwan


status: Public on Jan 10 2013

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

summary: Copy number profiling of 92 human lung tumors on Affymetrix 100K SNP arrays was conducted in order to assess the interaction of common genomic alterations with response to targeted anti-cancer therapeutics. Class 1 phosphatidylinositol 3' kinase (PI3K) plays a major role in cell proliferation and survival in a wide variety of human cancers. Here we investigate biomarker strategies for PI3K pathway inhibitors in non-small-cell lung cancer (NSCLC).   Molecular profiling of NSCLC tumor samples showed that copy number gains in PIK3CA and total loss of PTEN protein were common in squamous cell carcinoma samples, whereas LKB1 loss and mutations in KRAS and EGFR were common in adenocarcinomas. A panel of NSCLC cell lines characterized for alterations in the PI3K pathway was screened with PI3K and dual PI3K/mTOR inhibitors to assess the preclinical predictive value of candidate biomarkers.   Cell lines harboring pathway alterations (RTK activation, PI3K mutation or amplification, PTEN loss) were exquisitely sensitive to the PI3K inhibitor GDC-0941. A dual PI3K/mTOR inhibitor had broader activity across the cell line panel and in tumor xenografts. The combination of GDC-0941 with paclitaxel, erlotinib, or a MEK inhibitor had greater effects on cell viability than PI3K inhibition alone.    CONCLUSIONS: Candidate biomarkers for PI3K inhibitors have predictive value in preclinical models and show histology-specific alterations in primary tumors, suggesting that distinct biomarker strategies may be required in squamous compared with non-squamous NSCLC patient populations.

overall_design:
Lung tumors were profiled on Affymetrix GeneChip Mapping 100K Set Arrays
Tumor samples were profiled for copy number without any treatment of the tumor.

first: Carol

last: O'Brien

first: Jill

last: Spoerke

first: Jane

last: Fridlyand

middle: M

first: Mark

last: Lackner


title: Increased X-ray sensitivity and sustained chromosomal stability in Ataxia Telangiectasia-derived induced pluripotent stem (AT-iPS) cells

status: Public on Jun 22 2013

first: Akihiro

last: Umezawa

summary: Disease-specific induced pluripotent stem (iPS) cells have been used for a model to analyze pathogenesis of the disease. In this study, we generated iPS cells derived from a fibroblastic cell line of ataxia telangiectasia (AT-iPS cells), a neurodegenerative, inherited disease with chromosomal instability and hypersensitivity to ionizing radiation. AT-iPS cells exhibited hypersensitivity to X-ray irradiation, one of the characteristics of the disease. Surprisingly, while parental ataxia telangiectasia cells exhibited significant chromosomal abnormalities, AT-iPS cells did not show any chromosomal instability in vitro, i.e. maintenance of intact chromosomes at least by 80 passages (560 days) probably due to robust stability of pluripotent stem cells such as iPS cells and embryonic stem cells. The whole exome analysis also showed comparable nucleotide substitution speed in AT-iPS cells. Interestingly, after longer period of AT-iPS implantation into immunodeficient mice, teratoma generated by AT-iPS cells exhibited telangiectasia and carcinogenesis that are two characteristic symptoms of ataxia telangiectasia. Taken together, AT-iPS cells would be a good model for ataxia telangiectasia to clarify pathogenesis of the disease, and may allow us to facilitate development of drugs that inhibit ataxia and hypersensitivity to ionizing radiation for therapeutic application.

overall_design: The parental AT1OS fibroblast cells and four independent AT-iPS clones were subjected to Illumina HumanCytoSNP-12 v2.1 BeadChip analysis.

first: Masashi

last: Toyoda

first: Kazuhiro


title: Expression data of the Dongjin and osbzip58-1 mutants in the immature endosperm at 9 DAF

status: Public on Dec 31 2012

first: Wang

middle: Jie

last: Chen

state: Shanghai

address: 300 fenglin Road

institute: Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science

summary:
OsbZIP58 is a regulator of starch synthesis in rice endosperm. T-DNA insertion null mutants of this gene showed a white belly phenotype indicating an altered starch composition and content.
We further investigated how reduction of OsbZIP58 gene expression caused these changes by analyzing the transcriptomes in the immature endosperm at 9 DAF of the wild-type and osbzip58-1 mutants by microarray analysis.

overall_design: 9 DAF endosperm of Dongjin (wild type) and osbzip58-1 were used to compare the gene expresion, and three independent biological replicates for each material.

first: Xiu-ling

last: Cai

first: Jie-chen

last: Wang


title: High natural gene expression variation in the reef-building coral Acropora millepora: Potential for acclimative and adaptive plasticity

status: Public on Apr 08 2013

city: Miami

first: Anthony

middle: John

last: Bellantuono

state: FL

department: Biological Sciences

institute: Florida International University

summary: This experiment assessed the natural gene expression variation present between colonies of the Indo-Pacific reef-building coral Acropora millepora, and additionally explored whether gene expression differed between two different intron haplotypes according to intron 4-500 in a carbonic anhydrase homolog. This study found no correspondence between host genotype and transcriptional state, but found significant intercolony variation, detecting 488 representing unique genes or 17% of the total genes analyzed. Such transcriptomic variation could be the basis upon which natural selection can act. Underlying variation could potentially allow reef corals to respond to different environments. Whether this source of variation and the genetic responses of corals and its symbionts will allow coral reefs to cope to the rapid pace of global change remains unknown.

overall_design: A. millepora colonies were brought to a common garden in the reef lagoon, i.e. under the same environmental conditions. This common garden combined with acclimatization removes environmental effects on the physiology of the coral colonies. For the comparison of the two intron haplotypes, we applied a multiple dye-swap microarray design for the two groups of coral colonies (N=3 per group) defined based on the two genotypes resolved with the use of intron 4-500 (Fig. 1). To also examine the intra-haplotype variation we added a loop design nested to the above multiple dye-swap design, where three samples per colony were included. Colonies 1, 2, and 3 are of intron 4-500 haplotype 1; colonies 4, 5, and 6 are haplotype 2.

middle: J

first: Camila

last: Granados-Cifuentes


title: Elimination of mitochondrial DNA variants by nuclear genome transfer in human oocytes

status: Public on Dec 01 2012

city: New York

first: Dieter

last: Egli

state: NY

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

summary: Nuclear genome exchange between different oocytes results in efficient development and stem cell derivation

overall_design: 1 million cells was used for RNA extraction and labeling using the Illumina total prep RNA amplification kit. Parthenogenetic stem cell lines and embryonic stem cells

first: Daniel

last: Paull


title: The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment.

status: Public on May 26 2013

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

country: United Kingdom

institute: University of Cambridge

summary: Here we tracked transcriptome changes over ten human hematopoietic stem and early progenitor populations, defining the transcriptional dynamics underlying the first steps of commitment. Most of the transcriptional programs observed extended beyond lineage boundaries. In particular, multi-lymphoid progenitors (MLPs) presented a hybrid transcriptional state with elements of lymphoid and myeloid programs, but also stem cell characteristics.

overall_design: Total RNA was obtained from flow-sorted populations of human cord blood based on the cell surface expression of CD34, CD38, CD45RA, Thy1, and CD49f, CD10, CD7, CD19 and CD1a.

first: Sergei

last: Doulatov

first: Sasan

last: Zandi

first: Jian-Bing

last: Fan

first: John

middle: E

last: Dick


title: The genomic landscape of small intestine neuroendocrine tumors [CGH]

status: Public on Mar 16 2013

city: Rochester

first: Ganesh

last: Boora

state: MN

address: 200 First Street

institute: Mayo Clinic

summary: Small intestine neuroendocrine tumors are the commonest neuroendocrine tumors of the GI tract. Next gen sequencing of the whole exome was undertaken to identify SNPs and SCNA in these tumor samples. Subsequent bioinformatic anlaysis was done where the reads ratios of tumor/normal were log2 tranformed, segments indentified with DNAcopy (R package) and regions of SCNA were identified. Amplification of chr 4, 5, 14 and 20 was observed. The validation of these SCNAs was done with arrayCGH. The results of array CGH is in concordeance with the exome sequencing data.

overall_design:
DNA from matched tumor and normal sample of SI-NETs was done by spin column method. Libraries were constructed and exome enriched for next gen sequencing. The same gDNA was hybridized with Cy5 and Cy3 and subsequent analysis was done.

This study represents the CGH portion of the study.

first: G


title: affy_riz_2011_7-: Transcriptomic analysis of rice leaves challenged with virulent and avirulent Xoo strains

status: Public on Oct 15 2012

first: stephanie

last: huguet

summary: affy_riz_2011_7 - affy_riz_2011_7 - 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 (TTSS) that is devoted to the injection of type 3 effectors (T3Es) 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. During an incompatible interaction, T3Es may act as Avr proteins and stimulate Effector-Triggered-Immunity. We aim at evaluating the transcriptomic response of rice leaves challenged with avirulent strains of Xoo BAI3 and MAI1 on resistant lines IR64 and IRBB4 versus the reference susceptible rice line Nipponbare. In addition, we investigated the transcriptomic response of rice leaves upon inoculation of an XoohrcC mutant strain affected in the production of a functional TTSS.-The goal of the experiment is to characterize the rice leaf transcriptome response, upon the inoculation of susceptible and resistant rice leaves 24 hours post-infection. To that end, the experimental design includes the inoculation of susceptible Nipponbare rice leaves with Xoo strains BAI3 (race A1) and MAI1 (race A3), that will be compared to the response of resistant lines IRBB4 and IR64 rice lines. In addition, Nipponbare rice leaves will also be challenged with the BAI3hrcC mutant that is affected in the production of a functional TTSS.

overall_design: 18 arrays - rice; avirulent vs virulent

first: Boris

last: Szurek

first: Stephanie

last: Huguet

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: A microarray for assessing transcription from pelagic marine microbial taxa

status: Public on Mar 07 2013

city: Santa Cruz

first: Irina

last: Shilova

state: California

address: 1154 High str

department: Ocean Sciences

institute: UC Santa Cruz

summary: Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world’s oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.

overall_design: We analyzed RNA samples obtained from on-board incubations with phosphate and iron (III) after 48h.

first: Julie

last: Robidart

first: James

middle: H

last: Tripp

first: Kendra

last: Turk-Kubo

last: Wawrik

middle: T

last: Hollibaugh

first: Andy

last: Millard

first: Martin

last: Ostrowski

first: Ryan

last: Paerl

first: Anton

last: Post

first: David

last: Scanlan

first: Rhona

last: Stuart

first: Anne

last: Thompson

first: Bess

last: Ward

first: Jonathan

last: Zehr


title: Comparison of transcriptome profile between wild-type and dao mutant plants

status: Public on Sep 25 2012

city: Nanjing

first: Zhao

middle: Zhi

last: Gang

state: Jiangsu

address: Tongwei-load

department: Institute of Crop Science

institute: Nanjing Agricultural University

summary:
We identified and characterized that the rice Dioxygenase for Auxin Oxidation (dao) mutant displays pleiotropic phenotypes, including indehiscent anthers, sterile pollens, and increased free IAA levels in anthers.We conclude that DAO-mediated auxin catabolism is essential for auxin homeostasis and later stages of plant reproductive development, including anther dehiscence, and pollen viability.
We used microarrays to identify differentially expressed genes in dao.

overall_design: For genome-wide expression analysis of dao, three replicates of WT and dao samples (RNA from mature anthers) were analyzed on Affymetrix Genechip® Rice Genome arrays by an Affymetrix service facility (CapitalBio Corporation) according to the manufacturer’s protocols. Genes showing a 2-fold change with a q-value ≤ 0.05 were considered to be differentially expressed.

first: Zhigang

last: Zhao

first: Yunhui

last: Zhang

first: Jianmin

last: Wan


title: Expression data from IR64 rice transformed with 35S::OsPSTOL1 gene

status: Public on Sep 01 2012

city: Los Baños

first: Rico

last: Gamuyao

state: Laguna

address: College

department: Plant Breeding, Genetics, and Biotechnology Division

country: Philippines

institute: International Rice Research Institute

summary:
OsPSTOL1 confers phosphorus (P)-deficiency tolerance in rice through enhancement of early root growth. The larger root surface area at early stage provides the plants an advantage for nutrient uptake.
We conducted microarrays to determine the genes which are constitutively regulated by OsPSTOL1, independent of P supply and developmental stage.

overall_design: For Affymetrix microarrays, root RNA samples from IR64 35S::OsPSTOL1 plants (transgenic: T) and Nulls (non-transgenic: NT) grown in P-deficient soil +/- application of P fertilizer were used. Plants were at the reproductive/heading stage (- P treatment) and at mid-tillering (+P treatment), respectively.

first: Sigrid

last: Heuer


title: SNP data from human fibroblasts and induced Pluripotent Stem cells

status: Public on Jan 31 2013

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary:
Human induced Pluripotent Stem cells (hiPSc) and their differentiated progeny have great potential for modelling disease. To realise this potential, robust protocols need to be developed for deriving authentic differentiated cell lineages and these lineages need to be rigorously characterised. We have generated hiPSc using retrovirus-mediated delivery of reprogramming factors, and have used them for characterising mid-brain dopaminergic neurons. hiPSc lines have been screened using SNP array to assess chromosomal stability, and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets.
A mature physiological cellular model of human dopaminergic neurons.

overall_design: human iPSc lines were derived from normal human dermal fibroblasts.

first: E

last: Hartfield

first: M

last: Yamasaki-Mann

first: H

last: Fernandes

first: J

last: Vowles

first: W

middle: S

last: James

first: R

last: Wade-Martins


title: Expression data from rice organs at the reproductive stage

status: Public on Oct 13 2012

city: Yokohama

first: Hitoshi

last: Sakakibara

address: 1-7-22 Suehiro, Tsurumi

department: Plant Science Center

institute: RIKEN

summary:
Plant hormones interact with each other and regulate gene expression to control plant growth and development. To understand the complex network, accumulation of comprehensive and integrative data of gene expression and hormone concentration is important. Using microarray, global gene expression profile was analyzed to compare with plant hormone concentration in 14 parts of rice at reproductive stage.
The microarray data are used to construct public rice hormonome-transcriptome database UniVIO (http://univio.psc.riken.jp/).

overall_design: We analyzed flower, panicle branch,internode I, node I and II, and some leaves of rice plant at the heading satage. Total 35 samples were analyzed in this experiment.

first: Toru

last: Kudo

first: Nobue

last: Makita


title: Expression data in response to Xoo. bacterial infection in rice

status: Public on Feb 20 2013

city: Bundoora

first: Reena

last: Narsai

address: 5 Ring road

institute: La trobe University

summary:
In response to bacterial infection, early transcriptional re-programming occurs in the host plant.
We used microarrays to analyse the global transcriptomic response to Xoo. infection in a resistant rice cultivar (IR24). This was analysed in parallel with microarrays examining Xoo infection in a susceptible rice cultivar (IRBB21) as well as in response to Xoc [GSE19239], viral [GSE11025], parasite [GSE10373] and fungal [GSE7256, GSE18361] infections in rice, in order to identify common and distinct responses to biotic stress.

overall_design: Xoo (strain PXO71) was used to infect 35-day old plants (cv. IR24 and IRBB21) and leaf samples were collected at 24 h and 96 h after infection.


title: Intrinsic glioma subtypes in EORTC 26951 (part 6)

status: Public on Feb 01 2013

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

summary: Background: Intrinsic glioma subtypes (IGS) are molecularly similar tumors that can be identified based on unsupervised gene-expression analysis. Here, we have evaluated the clinical relevance of these subtypes within EORTC26951, a randomized phase III clinical trial investigating adjuvant procarbazine, CCNU (lomustine) and vincristine (PCV) chemotherapy in anaplastic oligodendroglial tumors. Our study is the first to include gene-expression profiles of formalin-fixed and paraffin-embedded (FFPE) clinical trial samples. Methods: Gene-expression profiling was performed in 140 samples: 47 fresh frozen and 93 FFPE, on HU133_Plus_2.0 and HuEx_1.0_st arrays (Affymetrix), respectively.  Results: All previously identified six intrinsic glioma subtypes are present in EORTC26951. This confirms that different molecular subtypes are present within a well-defined histological subtype. Intrinsic subtypes are highly prognostic for overall- (OS) and progression-free survival (PFS). They are prognostic for PFS independent of clinical (age, performance, tumor location), molecular (1p19qLOH, IDH1 mutation, MGMT methylation) and histological parameters. Combining known molecular (1p19LOH, IDH1) prognostic parameters with intrinsic subtypes improves outcome prediction (Proportion of Explained Variation 30% v 23%). Specific genetic changes (IDH1, 1p19qLOH and EGFR amplification) segregate into different subtypes. We identified one subtype, IGS-9 (characterized by a high percentage of 1p19qLOH and IDH1 mutations), that especially benefits from PCV chemotherapy. Median OS in this subtype was 5.5 years after radiotherapy (RT) alone v 12.8 years after RT/PCV; P=0.0349; HR 2.18, 95% CI [1.06, 4.50]. Conclusion: Intrinsic subtypes are highly prognostic in EORTC26951 and improve outcome prediction when combined with other prognostic factors. Tumors assigned to IGS-9 benefit from adjuvant PCV

overall_design: A total of 140 samples were included in this study, profiles of 95 were FFPE derived samples run on exon arrays. 12 samples (part 2) can also be found in GSE16011 (PMID 19920198 and 16357140), and 6 from Oncomine (part 3).

first: Lale

last: Erdem

first: Lonneke

last: Gravendeel

first: Johan

last: de Rooi

first: Paul

last: Eilers

first: Ahmed

last: Idbaih

first: Wim

middle: G

last: Spliet

first: Wilfred

middle: F

last: den Dunnen

first: Johannes

middle: L

last: Teepen

first: Pieter

last: Wesseling

first: Peter

last: Sillevis Smitt

last: Kros

first: Thierry

last: Gorlia

first: Martin

last: van den Bent


title: Comparative transcriptome profiling of chilling stress responsiveness in two contrasting rice genotypes

status: Public on Dec 21 2012

city: beijing

first: ting

last: zhang

state: beijing

address: zhongguancun south street 12

institute: Chinese Acadamy of agricultural science

summary:
Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in LTH, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in LTH and strong repression in IR29. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance.
In present study, comprehensive gene expression using an Affymetrix rice genome array revealed a diverse global transcription reprogramming between two rice genotypes under chilling stress and subsequent recovery conditions. The dominant change in gene expression at low temperature was up-regulation in the chilling-tolerant genotype and down-regulation in the chilling-sensitive genotype. Early responses to chilling stress common to both genotypes featured up-regulated genes related to transcription regulation and signal transduction, while functional categories of LR-chilling regulated genes were clearly diverse with a wide range of functional adaptations. At the end of the chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovery capacity at the transcriptional level. Finally, analysis of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, are involved in chilling stress tolerance.

overall_design: In this study, parallel transcriptomic analysis in two rice genotypes with contrasting chilling-tolerant phenotypes was performed to identify and characterize novel genes involved in chilling stress tolerance in rice.

first: Ting

last: Zhang

first: Xiuqin

last: Zhao

first: Yajiao

last: Pan

first: Liyu

last: Huang

first: Xiaoyue

last: Liu

first: Ying

last: Zong

first: Linghua

last: Zhu

first: Daichang

last: Yang

first: Binying

last: Fu


title: Transcriptome study of rice early response to rice blast fungus

status: Public on Dec 25 2012

city: Beijing

first: Tong

last: Wei

address: No. 5 Yiheyuan Road

institute: Peking University

summary:
Rice blast disease is a major threat to rice production worldwide, but the mechanisms underlying rice resistance to the causal agent Magnaporthe oryzae remain elusive.
In this whole-genome transcriptome study of rice early defense response to M. oryzae, we applied Affymetrix Rice Genome Genechip to compare the compatible and incompatible rice-M. oryzae interactions in 24 hours post-inoculation.

overall_design: Leaf samples were harvested from three biological replicates of fungal- and mock-inoculated seedlings at 24 hours post-inoculation, from which RNA were extracted and analyzed with Genechip Rice Genome Array.

first: Chengyun

last: Li

first: Genji

last: Qin

first: Li-Jia

last: Qu


title: Expression data from roots of rice seedlings

status: Public on Oct 31 2012

first: Wei-Hua

last: Wu

state: Beijing

address: No.2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

summary: Potassium (K+) is one of the most important nutrient ions in plant cells and play crucial roles in many plant physiological and developmental processes. K+ deficiency is the common abiotic stress in natural environment, which inhibits plant growth and reduces production of crops. We used microarrays to analyse the transcriptomic changes in rice roots after suffering K+ starvation at different times. The results of GO analysis showed that these transcriptionally changed genes mainly fell into the categories of metabolic process, membrane, cation binding, kinase activity, transport and so on.

overall_design: The two-week-old hydroponic rice seedlings were transferred to K+-free solution (-K) and K+-replete solution (+K, 1 mM K+) as treatment (LK) and control (CK) conditions respectively. The fresh roots of both control and treated rice seedlings were collected after K+-deficient treatment at indicated times (6 h, 3 d and 5 d). The roots were frozen immediately using liquid nitrogen and stored at -80℃ for further RNA extraction. Every RNA sample was derived from 5 independent seedlings. In sum, three time points were selected and three biological replicates were performed at each time point, totally 18 rice genome arrays were used.

first: Tian-Li

last: Ma

first: Yi

last: Wang


title: Genome-wide Gene Expression Profiling Associated with Seedling Cold Tolerance Improvement in Japonica Rice Background

first: Fan

address: 12 South Zhong-Guan-Cun St.

institute: CAAS

summary:
Rice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage resulting in poor growth and yield loss. In general, japonica rice has stronger cold tolerance (CT) than indica rice. However, several favorite alleles for CT exist in indica rice and can be used to enhance CT under japonica background.  Genome-wide gene expression profiling is the efficient way to decipher the molecular genetic mechanism of CT enhancement and provide valuable information for the CT improvement in rice molecular breeding.
In this study, the transcriptome of a CT introgressed line (IL) K354 and its recurrent parent C418 under cold stress were comparatively analyzed to explore the possible CT enhancement mechanism of K354.Totally 3184 differentially expressed genes (DEGs) including 195 transcription factors were identified in both lines under cold stress, about half of them were commonly regulated, which were involved in the major cold responsive pathways including OsDREB1s regulon. The K354-specific cold-induced DEGs were mainly related to stimulus response, cellular cell wall organization, and microtubule-based movement process compared with commonly cold-induced DEGs by GO analysis. Moreover, 296 constitutive DEGs with significantly different transcription level between C418 and K354 were detected under both control and cold stress conditions. K354-specific cold-regulated and constitutive DEGs jointly account for the CT improvement of K354. Pathway analysis unraveled up-regulation of starch and sucrose metabolism in both genotypes and presumably weaker defense response to stress in K354 than C418 under cold stress. Candidate genes prediction based on previous putative CT genetic networks revealed genotype-dependent CT enhancement mechanism in CT IL K354 vs recurrent parent C418, including Sir2, OsFAD7, OsWAK112d, and PCD related genes, etc.We propose a hypothesis of the CT enhancement mechanism in rice based on the results in present study. Firstly, a number of cold-regulated genes are able to express constitutively at high level or absent under control condition for standing by the arrival of cold stress. Next, under cold stress slower perception of stress signal from the more cold-tolerant membrane can postpone the activation of defensive system which may have possible negative effects on rice growth. Then, PCD will be launched to sacrifice a few cells for maintaining the basal growth of most cells. Finally, the protective responses on multiple aspects of cold damage will be postponed because of delayed several cold-defensive pathways (i.e. OsDREB1C regulon). It might explain why the recovery capacity of K354 from cold stress to control condition is stronger than C418. The CT enhancement mechanism can be regarded as the possible way to improve CT of japonica rice using indica germplasm in rice breeding program.

overall_design: In this study, the specific gene expression patterns of two genotypes (C418 and K354) at 2h, 6h, 12h, 24h and 48h during cold stress treatment (4 C) and control were characterized by using the Affymetrix rice microarray platform.

first: Li-Yu

first: Wen-Sheng

first: Xiu-Qin

first: Ling-Hua

first: Bin-Ying

first: Zhi-Kang


title: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (SNP data)

status: Public on Aug 01 2012

city: Pamplona

first: Vicente

middle: Jose

last: Fresquet

state: Navarra

address: Av Pio XII 55

department: Division of Oncology

country: Spain

institute: Center for Applied Medical Research (Cima)

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

summary: Using high-resolution genomic microarray analysis, a distinct genomic profile was defined in 114 samples from patients with splenic marginal zone lymphoma (SMZL). Notably, deletion or uniparental disomy of chromosome 7q were detected in 39% of SMZLs but in only 9 of 170 (5%) mature B-cell lymphomas (p<10-6). The presence of unmutated IgVH genes, genomic complexity, 17p13-P53 deletion and 8q gain including MYC gene, but not 7q deletion, were correlated with shorter overall survival. Extensive mapping analyses narrowed down the commonly deleted region to 2.7 Mb. in 7q32.1-q32.2 from SND1 to COPG2 genes. High-throughput sequencing analysis of the 7q32 deleted segment in SMZL cells did not identify bi-allelic deletions, insertions or clear pathogenic mutations, but detected six single nucleotide changes in IRF5 (n=2), TMEM209 (n=2), CALU (n=1) and ZC3HC1 (n=1). Comparative expression analysis found that IRF5, TMEM209 and CALU genes had down-regulated expression in lymphomas with 7q32 deletion vs. non-deleted tumors. Ectopic expression of IRF5 in marginal-zone lymphoma cells decreased cell proliferation and induced apoptosis. These results indicate that small deletions, insertions and/or point mutations inactivating genes within 7q32 are not common events in SMZL. Further studies are required to evaluate the putative role of IRF5 in SMZL pathogenesis.

overall_design: Affymetrix GeneChip 50k-XbaI and/or 250-NspI/StyI SNP microarrays were performed for 59 SMZL samples and 4 Marginal Zone cell lines according to the manufacturer's directions.

first: Eloy

last: Robles

first: Anton

last: Parker

first: Javier

last: Martinez-Useros

first: Maria

last: Mena

first: Raquel

last: Malumbres

first: Lorena

last: Fontan

first: Jose

middle: I

last: Martinez-Ferrandis

first: Xabier

last: Aguirre

first: Susana

last: Catarino

first: David

last: Arteta

first: Lourdes

last: Osaba

first: Manuela

last: Mollejo

first: Jesus

last: Hernandez-Rivas

last: Calasanz

first: Masanori

last: Daibata

first: A

last: Karpas

first: Martin

last: Dyer

first: Felipe

last: Prosper

first: Esperanza

last: Vizcarra

first: Miguel

last: Piris

last: Oscier

last: Martinez-Climent


title: Comparison of transcriptional responses of two susceptible rice cultivars to strains of Xanthomonas oryzae

status: Public on Mar 06 2012

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

summary:
X. oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight of rice.  X. oryzae pv. oryzicola (Xoc) is the causal agent of bacterial streak of rice.  Fourteen day old rice leaves were inoculated with one of five strains of Xanthomonas oryzae. Seven strains of Xoo were used; three wild type strains (PXO99A, T7174, and PXO86) and strains PXO99AME7, which has a nonfunctional type III secretion system and is non-pathogenic, , PXO99AME1, a pthXo6 and avrXa27 double mutant, PXO99ME2, a pthXo1 mutant, and PXO99ME5, a reduced virulence strain with uncharacterized mutation in a TAL effector.  One strain of Xoc (BLS303) was tested.  Controls include an inoculation with water (MOCK) and no inoculation.  T7174 is our label for the Japanese isolate MAFF311018.  Third leaves are inoculated with a needless syringe at adjacent sites along the upper leaf blade.  Six leaves from separate plants are pooled.  RNA samples were collected 24 h after treatment.

 ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Ginny Antony.  The equivalent experiment is OS66 at PLEXdb.]

overall_design: cultivar: Nipponbare - strain: PXO99A(3-replications);  cultivar: Nipponbare - strain: PXO99AME7(3-replications);  cultivar: Nipponbare - strain: PXO99AME5(3-replications);  cultivar: Nipponbare - strain: MOCK(3-replications);  cultivar: Nipponbare - strain: NO TREATMENT(2-replications);  cultivar: Nipponbare - strain: T7174(3-replications);  cultivar: Nipponbare - strain: PXO86(3-replications);  cultivar: Nipponbare - strain: BLS303(3-replications);  cultivar: Nipponbare - strain: PXO99AME1(3-replications);  cultivar: Nipponbare - strain: PXO99AME2(3-replications);  cultivar: Nipponbare - strain: PXO99A-2(3-replications);  cultivar: IR24 - strain: PXO99A(3-replications);  cultivar: IR24 - strain: PXO99AME7(3-replications);  cultivar: IR24 - strain: PXO99AME5(3-replications);  cultivar: IR24 - strain: MOCK(3-replications);  cultivar: IR24 - strain: NO TREATMENT(3-replications);  cultivar: IR24 - strain: T7174(3-replications);  cultivar: IR24 - strain: PXO86(3-replications);  cultivar: IR24 - strain: BLS303(3-replications);  cultivar: IR24 - strain: PXO99AME1(3-replications);  cultivar: IR24 - strain: PXO99AME2(3-replications);  cultivar: IR24 - strain: PXO99A-2(3-replications)

first: Ginny

last: Antony

first: Frank

last: White


title: Nitrogen-efficient rice over-expressing alanine aminotransferase

status: Public on Jul 27 2012

city: Edmonton

first: Perrin

middle: Hudson

last: Beatty

state: Alberta

address: G425 Biological Sciences

country: Canada

institute: University of Alberta

summary:
Oryza sativa cv. Nipponbare was engineered to over-express a barley alanine aminotransferase (alaAT) gene using the promoter (OsANT1) from a rice aldehyde dehydrogenase gene that expresses in roots.
We are using biotechnology to improve the nitrogen use efficiency of rice by over-expressing alaAT in a tissue specific (root) manner. The AlaAT enzyme is a reversible aminotransferase that is linked to both C and N metabolism since it uses pyruvate plus glutamate to produce alanine and 2-oxoglutarate, and visa versa.

overall_design: Wildtype rice (Nipponbare) and three independent OsANT1:HvAlaAT rice transgenic lines (AGR1/7, AGR1/8 and AGR3/8) were grown hydroponically with 5mM NH4+ as the nitrogen source, to the reproductive stage. RNA samples were taken at active tillering, maximum tillering and end-of-tillering stages from root and shoot, at mid-day of the plants' day/night cycle. The RNA from root and shoot at maxiumum tillering was used for microarray analysis. Please read Beatty et al., 2009, Plant Biotechnology Journal 7, pp562-576 for further details..

first: Ashok

middle: K

last: Shrawat

first: Rebecka

last: Carroll

first: Tong

last: Zhu

first: Allen

last: Good


title: Comparative Transcriptomes Profiling of Photoperiod-sensitive Male Sterile Rice Nongken 58S between Short Day and Long Day Condition

status: Public on Jul 30 2012

city: wuhan

first: Wei

last: Wang

address: Bayi Road

institute: Wuhan Universtiy

summary:
Nongken 58S is photoperiod-sensitive genic male sterile (PGMS) rice. Its pollens are fully sterile when it is treated with LD condition from glume primordium differentiation stage to pistil/stamen primordium forming stage, and its pollens are fertile when treated with SD condition during these stages.
We used microarrays to detail the global programme of leaf gene expression under LD and SD condition for investigating the transcriptomes in the male sterility transition in PGMS rice to find out the genes related to this transition

overall_design:
We compared the transcriptomes of Nongken 58S under shortday (SD) and longday (LD) at the glume primordium differentiation stage and pistil/stamen primordium forming stage, respectively. 12 samples were analyzed, and each treatment had biological triplicates.

Supplementary files: SD vs LD during the glume primordium differentiation stage and the pistil/stamen primordium forming stage.

first: Zhenwei

last: Liu

first: Zhibin

last: Guo

first: Gaoyuan

last: Song

first: Qin

last: Chen

first: Daiming

last: Jiang

first: Yingguo

first: Daichang

last: Yang


title: Comparison of transcriptome profile between wild-type and Epi-df mutant plants

status: Public on Jul 13 2012

first: Liguo

last: Zhang

address: South Zhongguancun Street

institute: Chinese Academy of Agricultural Sciences

summary:
We identified and characterized a rice epigenetic mutant Epi-df which exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We demonstrated that Epi-df participates in Polycomb repressive complex 2 (PRC2) mediated gene silencing. Epigenetic mutations results in ectopic expression of Epi-df and pleiotropic developmental defects in mutant plants. Moreover, ectopic expression of Epi-df leads to mis-regulated H3K27me3 and changed expression of hundreds of genes involved in a wide range of biological processes.
We used microarrays to identify differentially expressed genes in Epi-df.

overall_design: For genome-wide expression analysis of Epi-df, three replicates of WT and Epi-df samples (RNA from 3-week-old seedlings) were analyzed on Affymetrix Genechip® Rice Genome arrays by an Affymetrix service facility (CapitalBio Corporation) according to the manufacturer’s protocols. Genes showing a 2-fold change with a q-value ≤ 0.05 were considered to be differentially expressed.

first: Zhijun

last: Cheng

first: Jianmin

last: Wan


title: Expression profiling of lower-grade diffuse astrocytic glioma

status: Public on Feb 24 2012

first: Jason

last: Huse

institute: Memorial Sloan-Kettering Cancer Center

summary: Diffuse gliomas represent the most prevalent class of primary brain tumor.  Despite significant recent advances in the understanding of glioblastoma (WHO IV), its most malignant subtype, lower-grade (WHO II and III) glioma variants remain comparatively understudied, especially in light of their notably variable clinical behavior.  To examine the foundations of this heterogeneity, we performed multidimensional molecular profiling, including global transcriptional analysis, on 101 lower-grade diffuse astrocytic gliomas collected at our own institution, and validated our findings using publically available gene expression and copy number data from large independent patient cohorts.  We found that IDH mutational status delineated molecularly and clinically distinct glioma subsets, with IDH mutant (IDH mt) tumors exhibiting TP53 mutations, PDGFRA overexpression, and prolonged survival, and IDH wild-type (IDH wt) tumors exhibiting EGFR amplification, PTEN loss, and unfavorable disease outcome.  Furthermore, global expression profiling revealed three robust molecular subclasses within lower-grade diffuse astrocytic gliomas, two of which were predominantly IDH mt and one almost entirely IDH wt.  IDH mt subclasses were distinguished from each other on the basis of TP53 mutations, DNA copy number abnormalities, and links to distinct stages of neurogenesis in the subventricular zone (SVZ).  This latter finding implicates discrete pools of neuroglial progenitors as cells of origin for the different subclasses of IDH mt tumors.  In summary, we have elucidated molecularly distinct subclasses of lower-grade diffuse astrocytic glioma that dictate clinical behavior and demonstrate fundamental associations with both IDH mutational status and neuroglial developmental stage.

overall_design: 80 tumor samples, one normal tissue sample (brain)


title: Expression data from rice seeds during low temperature treatment

status: Public on Feb 19 2012

city: Shanghai

first: Hong-Wei

last: Xue

address: 300 Fenglin Road

institute: Institute of Plant Physiology and Ecology,Shanghai Institutes of Biological Sciences

summary:
As a species mostly planted in tropical and subtropical regions, rice is sensitive to chilling temperature, especially at reproductive stage. However, the effect of low temperature on seed development has not been well characterized.
The transcriptome of two rice cultivars Zhonghua11 and Hanfeng were analyzed to characterize the gene regulatory networks of rice seed during low temperature treatment.

overall_design: Whole plants of two rice cultivars Zhonghua11 (low temperature sensitive) and Hanfeng (low temperature tolerance) were treated at 14°C for 2 days during seed development stage. The plants without treatment serve as controls. Rice seeds were harvested for RNA extraction.

first: Liang-Jiao

first: Jing-Jing


title: Expression data from rice embryo and endosperm development

status: Public on Feb 01 2012

institute: Institute of Plant Physiology and Ecology,Shanghai Institutes for Biological Sciences

summary:
The receptor-like kinases (RLKs) plays critical roles in signal transduction through sensing the extracellular signals and activating the downstream signal transduction by phosphorylating their targets. Up to now, there are only a few RLKs have been functionally identified.
In this study, we systemically analyzed the expression pattern of rice genes, especially the RLK coding genes during embryo and endosperm development.

overall_design: Rice Ovary and three development stages of embryo and endosperm (embryo 3, 9, 12 DAF; Endosperm 3, 9, 16 DAF) were analyzed, all of them were biologically repeated two times.

first: Hong-wei

first: Lin-lin

last: Gao


title: GATA Transcription Factor (CGA1) Regulates Chloroplast Development in Rice

status: Public on Nov 06 2012

city: guelph

first: Yong Mei

last: Bi

address: 50 Stone Road E.

department: Molecular and Cellular Biology

institute: University of Guelph

summary:
A transcription factor CYTOKININ-RESPONSIVE GATA FACTOR 1 (CGA1) regulates chloroplast development in rice (Oryza sativa) through modifying the expression of important nuclear expressed, chloroplast localized genes.
A transcriptome analysis was done in wild type plants and transgenic rice over-expressing this OsCGA1 to identify the set of genes with altered expression.

overall_design: RNA was extracted from leaves of 4-wk old wild type and OsCGA1 overexpressing rice plants and hybridized to Affymetrix Rice Genome Array. Three biological replicates were sampled for wild type and OX plants.

first: Darryl

last: Hudson

first: David

last: Guevara

first: Andrew

last: Hand

first: Lixin

last: Hao

first: Xi

first: Tong

first: Yong-Mei

first: Steven

last: Rothstein


title: Expression data of one-week-old rice seedlings exposed to Pi-deficient solution for 6, 24, 48, 72 hours

status: Public on Jun 18 2012

first: xiaoyan

last: dai

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, the Chinese Academy of Sciences

summary: Expression profiles of one-week-old rice seedlings exposed to Pi-deficient solution for 6, 24, 48, 72 hours were monitored by microarray that contains approximately 60,000 rice clones (Affymetrix GeneChip). The probes were prepared from RNAs isolated from rice seedlings exposed to Pi-deficient solution for 6, 24, 48, 72 hours, respectively, and those non-treated controls. For hybridization, two biological replicates were used to extract RNAs from different batches of plants.

overall_design: Rice seedlings were exposed to low phosphate for 6h, 24h, 48h and 72 h, respectively. The Pi-inducible and Pi-repressive genes were taken as the expression ratio (treatment relative to control) greater and less than 2-fold, respectively


title: Genome-wide gene expression profiling of rice Zhonghua11 and ila1 lamina joint

status: Public on May 01 2012

first: Baocai

state: Beijng

address: Beichen west road

department: Center for Genome Biology

institute: Institute of Genetics and Developmental Biology, CAS

summary:
The leaf lamina joint joins the rice leaf blade and sheath, contributing significantly to the leaf angle trait. A more erect leaf facilitates the penetration of sunlight, enhancing photosynthetic efficiency and occupying less space in dense planting. Genetic screening found a mutant increased leaf angle1, ila1 from rice T-DNA insertional mutants library.
We used microarrays to detail the transcriptional profile changes in the mutant ila1 lamina joint.

overall_design: Two biological replicate sample of leaf lamina joints from the ila1 and wild-type plants at tillering stage were collected for RNA extraction. Total RNAs were isolated from each replicate via the TRIzol method (Invitrogen) and used in target synthesis for the Rice Genome Array from Affymetrix. The microarray analyses were performed through following standard protocols (Affymetrix).

first: Jing

last: Ning

first: Yihua

last: Zhou

first: Lizhong

last: Xiong


title: Expression profile of high yielding rice introgression line

status: Public on Dec 31 2011

city: Hyderabad

first: Sarla

last: Neelamraju

state: Andhra Pradesh

address: Rajendranagar

department: Crop Improvement Section

institute: Directorate of Rice Research

summary:
Leaves and  panicles from recurrent parent KMR3 and a high yielding KMR3-O.rufipogon introgression line were used
Microarray analysis was carried out to reveal up- and down-regulated DEGs in leaves and panicles of control and experimental line for identifying key genes that help improve yield

overall_design: Leaves and fully emerged young panicles from both lines were used for RNA extraction and hybridization on Affymetrix microarrays

first: N

last: Sarla

first: Rajeshwari

last: Ramanan


title: Gene expression in mature pollen and sperm cells versus young seedling as a vegetative sporophyte reference control

status: Public on Apr 30 2012

city: Norman

first: Scott

middle: D

last: Russell

state: OK

address: 770 Van Vleet Oval

department: Dept of Microbiology and Plant Biology

institute: University of Oklahoma

summary:
Sperm cells represent the male partner that fuses with the egg cell during fertilization in all multi-cellular eukaryotic organisms, and, in flowering plants, is a founder of both embryo and nutritive endosperm.  We examined the transcriptome of Oryza sativa ssp. japonica using the Affymetrix 57K rice genome GeneChip to provide an overview of genes activated in the paternal gamete.

We used microarrays to detail the global program of gene expression in mature pollen and sperm cells at anthesis, which constitutes the stage immediately preceding pollen germination and gamete deposition leading up to fertilization.  This documents the condition of the male gametophytic cells prior to fertilization.

Keywords: tissue expression profile, male gametophyte, sperm, pollen, seedling

overall_design: Male gametophytic cells consisting of isolated pollen and isolated sperm cells collected at anthesis were compared with seedlings containing leaf, stem, root and apical meristems as a vegetative sporophytic control; three separate biological replicates were used.

first: Xiaoping

last: Gou


title: Gene expression profiling of archival tongue carcinoma and normal tongue tissue (subset)

status: Public on May 11 2012

city: Umea

first: Matilda

last: Rentoft

address: NUS

department: Medical Biosciences

country: Sweden

institute: Umea University

summary: RNA extracted from 78 FFPE tongue samples, 62 tongue carcinomas and 16 non-malignant controls, were succesfully analysed using the whole genome DASL array to obtain gene expression profiles. Gene expression profiles were used to identify differentially expressed genes with the ultimate goal of finding out their importance for tongue cancer development and maintenance. Sample were formalin fixed paraffin embedded biopsies taken for diagnostic purposes and had been stored between 1 and 13 years. Because of the general poor quality of RNA from archival samples a special focus were put on its effect on the detected expression levels. 28 tumours and 16 controls with a CTdiff< 5 were selected for differential gene expression analysis. Raw data for only these samples were normalized again. Data for these 44 samples can be found here.

overall_design: Total RNA from formalin fixed paraffin embedded sample was extracted using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol. Quality of FFPE sample were evaluated by comparing how well a kousekeeping gene (TUBA6) could be amplified using q-PCR in each FFPE sample compared to two fresh frozen sample (Ctdiff= CTffpe-Ctff). The  DASL platform (cDNA-mediated annealing, selection, extension, and ligation assay) was used together with the whole genome arrays to obtain expression data for 20 818 genes.

first: Eva

last: Jonsson

first: Göran

last: Laurell

first: Philip

last: Coates

first: Karin

last: Nylander


title: Rice gene global expression analysis upon inoculation with different Magnaporthe isolates

status: Public on Mar 27 2012

city: LODI

first: PAMELA

last: ABBRUSCATO

state: LO

address: via Einstein

department: RICE GENOMICS UNIT

country: Italy

institute: PARCO TECNOLOGICO PADANO

summary:
Magnaporthe oryzae is the causative agent of the rice blast, the most relevant rice disease worldwide. To date expression analysis on rice infected with Magnaporthe oryzae have been carried out only with the strains FR13 (leaf) and Guy 11 (root). However different strains of Magnaporthe are present in the environment leading to different rice responses at molecular level. To gain more insight on the unknown molecular mechanisms activated by different Magnaporthe strains during rice defense, a global expression analysis was performed by using the GeneChip® Rice Genome Array.
To identify rice genes differentially regulated upon infection by Magnaporthe isolates, inoculation with different strains were performed and samples were collected 24 hours post infection.

overall_design: RNA were obtained from leaf samples after inoculation of rice 2 week-old plantlets with the following strains: rice isolates Magnaporthe oryzae FR13 and CL367, non-adapted strain BR32, isolated from wheat, and Magnaporthe grisea BR29 isolated from crabgrass. Treated and control (mock) rice leaves (cv. Nipponbare) were collected 24 hours post inoculation. Three biological replicates for each interaction type and the corresponding mock were extracted and analysed independently with the GeneChip® Rice Genome Array.

first: Pamela

last: Abbruscato

first: Odile

last: Faivre-Rampant

first: Marcello

last: Del Corvo


title: Rice gene global expression during nonhost interaction with Blumeria graminis f. sp. hordei (Bgh)

summary:
Powdery mildew is a very common plant disease and only few plants are immune. Host interactions have been identified and characterized for the pathosystems barley-B. graminis f. sp. tritici (Bgt) and wheat-B. graminis f. sp. hordei (Bgh), whereas no data are reported about powdery mildew and nonhost plants, such as rice. On the other hand rice nonhost resistance is widely unexploited and only few expression data are available. To characterize rice response during nonhost interaction with Bgh, a global expression analysis was performed by using the GeneChip® Rice Genome Array.
To describe rice gene expression profiles during nonhost interaction, 2 week-old rice plantlets were inoculated with Bgh. Treated (inoculated) and control (mock) samples were collected 24 hours post-inoculation for GeneChip® Rice Genome Array hybridization.

overall_design: For transcript proﬁling experiments with powdery mildew, entire leaves were sampled from rice plantlets 2 weeks old (cv. Nipponbare). Treated and control (mock) rice leaves were collected 24 hours post inoculation. Three biological replicates for inoculated and control plants were extracted and analysed independently with the GeneChip® Rice Genome Array.


title: Expression data from infected (Xanthomonas oryzae pv. Oryzae (P10)) leaf in japonica rice (cv. Y73)

status: Public on Feb 27 2012

city: Hangzhou

first: Xuming

last: Wang

state: Zhejiang

address: Shiqiao Road 198#

department: Institute of Virology and Biotechnology

institute: Zhejiang Academy of Agricultural Sciences

summary:
Previously, we successfully introduce the bacterial blight resistance trait from Oryza meyeriana into O. sativa using asymmetric somatic hybridization with O. meyeriana as the donor species. After years of breeding, a progeny named Y73 was generated with recurrent parent O. sativa L. ssp. japonica cv. Dalixiang, and it shows high resistance to broad-spectrum of bacterial blight pathogens Xanthomonas oryzae pv. Oryzae (Xoo). However, the resistance mechanism of Y73 is remain undiscovered. To provide insights into the high resistance phenotype of these plants, we examined the transcriptome response in leaves of Y73 to the bacterial blight infection in this study. Xoo inoculated and mock inoculated rice plants were grown in growth room and the global analysis of gene expression events in rice leaves at 24 hours post inoculation (hpi) were analyzed using Affymetrix Rice GeneChip microarrays.
We used microarrays to detail the global programme of gene expression underlying Xoo infection in rice Y73.

overall_design: To find out pathways and genes involved in its high and board-spectrum resistance, microanalysis were carried out on Y73 after Xoo infection at 24 hours post inoculation (hpi). Three independant replicates were perfomed for each treatments.

first: Jianping

last: Chen


title: Gene expression profiling of archival tongue carcinoma and normal tongue tissue

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

overall_design: Refer to individual Series


title: Expression data from OsRP1L1-overexpressing plant leaf in japonica rice (cv. Ishikari-shiroge (I-S))

summary: A novel rice NBS-LRR gene was cloned and overexpressed to explore its function in bacterial blight (BB) resistance. Due to its similarity to the Rp1 gene in maize (Zea mays), it was designated as OsRP1L1. We used microarrays to detail the global reprogram of gene expression in OsRP1L1-overexpressing plants.

overall_design: To find out pathways and genes related to this defense-related gene, microanalysis were carried out on OsPR1L1-overexpressing plants. Three independent replicates were perfomed for overexpressing plants and wild type plants.


title: Gene expression profiling of archival tongue carcinoma and normal tongue tissue (all samples)

summary: RNA extracted from 78 FFPE tongue samples, 62 tongue carcinomas and 16 non-malignant controls, were succesfully analysed using the whole genome DASL array to obtain gene expression profiles. Gene expression profiles were used to identify differentially expressed genes with the ultimate goal of finding out their importance for tongue cancer development and maintenance. Sample were formalin fixed paraffin embedded biopsies taken for diagnostic purposes and had been stored between 1 and 13 years. Because of the general poor quality of RNA from archival samples a special focus were put on its effect on the detected expression levels. 28 tumours and 16 controls with a CTdiff< 5 were selected for differential gene expression analysis. Data for only these sample were normalized again and can be found in seperate data file.


title: Global gene expression profiles of Oryza sativa wild type Nipponbare and mutant coi1-13

status: Public on Dec 01 2011

first: Li

last: Qun

state: Shanghai

department: National Key Laboratory of Plant Molecular Genetics

institute: Institute of plant physiology & ecology, SIBS, CAS

summary: To reveal the underlying molecular mechanism of jasmonate inhibits gibberellins signaling in rice, we performed transcriptional profiling of wild type nipponbare and mutant coi1-13 plants on a global scale using the Affymetrix GeneChip Rice Genome Array

overall_design: Rice young uppermost internodes were harvested and three biological repeats were performed on Nippombare (wild-type) and coi1-13 (mutant), respectively.

first: Yang

last: Donglei

first: He

last: Zuhua


title: Express data from rice endosperm

status: Public on Dec 06 2011

city: Mississippi State

first: Feng

last: Tan

state: MS

address: Dorman Hall 402

department: Biochemistry and Molecular Biology

institute: Mississippi State University

summary:
Immatured rice seeds 7-8 days after pollination were used for expression analysis and matured rice leaf was used as control.
Targets from biological replicates of both were generated and the expression were determined using Affymetrix Rice Genome arrays.

overall_design: Rice immatured seed after 7-8 days pollination were selected of early development for RNA extraction and hybridization on Affymetrix microarrays. Matured rice leaf was set as control. Each with 3 replicates were analyzed.

first: Juliet

last: Tang

first: Guosheng

last: Li

first: Brandon

last: Malone

first: Susan

last: Bridges

first: Zhaohua

last: Peng


title: Expression data from LRK1 060615 transgenic rice and control 9311

status: Public on Feb 12 2012

city: shanghai

first: Mengfei

last: Yang

address: Handan Road 220

institute: Fudan university

summary:
Plant height is a critical constituent of plant architecture. Rice (Oryza sativa) plants have the potential to undergo rapid internodal elongation, which determines plant height. A number of physiological studies have proved that gibberellin is involved in internode elongation. Leucine-rich repeat receptor-like kinases (LRR-RLKs) are the largest subfamily of transmembrane receptor-like kinases in plants. Plant LRR-RLKs play important functions in mediating a variety of cellular processes and regulating responses to environmental signals.
LRK1, a PSK receptor homolog, is a member of the LRR-RLK family. In the present study, differences in ectopic expression of LRK1 were consistent with extent of rice internode elongation. Analyses of gene expression demonstrated that LRK1 restricts gibberellin responsiveness during the internode elongation process by down-regulation of the gibberellin biosynthetic gene, ent-KAURENE OXIDASE (OsKO2).

overall_design: Leaf tissues of 6-week-old LRK1 060615 transgenic rice and control 9311 rice (10 plants each) were selected.

first: Jinshui


title: Affymetrix SNP array data for acute lymphoblastic leukemia and lymphoblastic lymphoma samples

status: Public on Jun 30 2012

city: Monza

first: Antonella

last: Lettieri

address: via Pergolesi 33

institute: Tettamanti Research Center

summary: Childhood T-cell malignancies include T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LBL).  T-ALL and  T-LBL share common morphologic and immunophenotypic features and are treated with similar therapeutic approaches. Nonetheless, they show distinct clinical presentations suggesting that they may represent two different biological entities. In order to investigate the common and unique genetic aberrations of T-LBL and T-ALL, copy number alteration (CNA) analysis was performed on a subset of the samples analyzed by GEP

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from diagnostic bone marrow aspirates or tumor tissue samples.
Copy number analysis of Affymetrix 100K SNP arrays was performed for 9 T-ALL and 9 T-LBL pediatric samples. The samples from leukemia/lymphoma remission were used as references for copy number inference.

first: Y

last: Nannya

first: H

last: Bengtsson

first: E

last: Venkatraman


title: Gene expression variation in horse placental and fetal tissue, and resting and stimulated horse lymphocytes

status: Public on Feb 14 2012

city: Ithaca

first: Donald

last: Miller

state: NY

address: Hungerford Hill Rd.

department: Baker Institute for Animal Health

institute: Cornell University

first: Douglas

last: Antczak


title: Gene Expression Profiling during Male Gametophyte Development in Rice

status: Public on Mar 15 2012

city: Chengdu

first: Sheng-hua

last: Wang

state: Sichuan

address: No.24 South Section 1, Yihuan Road

department: College of Life Science

institute: Sichuan University

summary: To investigate the potential function of miRNAs during male gametogenesis in rice, we first obtained gene expression profiles by using Affymetrix microarray technologies. In genome-scale, we found a common characteristic shared by rice and Arabidopsis, which vast of genes are down regulated from Pb to Pc stage. next, a total of 13363 genes were detected during the gametophyte development in rice, which contains 2925 pollen-enriched/-specific genes including 107 transcription factors. We also analyzed the microarray-based expression patterns of genes in miRNA pathways, and found 3 pollen-specific AGO genes (AGO12, AGO13 and AGO17).

overall_design: This subseries contains three datasets of gene expression in pollen development stages: uninucleate microspore (UNM/Pa), bicellular pollen (BCP/Pb) and tricellular pollen (TCP/Pc)

first: Hua

first: Jun

last: Chun

first: Tao-bo

last: Ai

first: Yong-ao

last: Tong


title: Somatic mutations in Liver Cancer

status: Public on Jan 19 2012

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary: Hepatocellular carcinoma tumor samples were profiled for chromsomal copy number changes on Affymterix 100K SNP arrays

overall_design: Analysis of copy number changes in Hepatocellular Carcinoma

first: Zhaoshi

last: Jiang

first: Suchit

last: Jhunjhunwala

first: Zora

last: Modrusan

middle: M

first: Zemin

last: Zhang


title: DNA microarray data from transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)

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: DNA microarray analysis has been proved to be an effective method in investigating unintended effects in genetically modified (GM) crops. But the distribution of differentially expressed genes in GM crops remains unclear. So the results of microarray analysis might be invalid for assessment of unintended effects if differentially expressed genes are extremely distributed. We used microarrays to study the distribution pattern of differentially expressed genes in HH1 at different developmental stages and environmental conditions.

overall_design: Samples were collected from both HH1 and MH63 at different developmental stages and environmental conditions and were used for RNA extraction and hybridization on Affymetrix microarrays. We selected differentially expressed genes, common differentially expressed genes and common significantly changed pathways hoping to clarify the distributions of differentially expressed genes in HH1.

first: Fangjun

last: Qi

first: Zhi

last: Liu


title: Gene expression profiling of rice embryogenic calli after Agrobacterium infection

status: Public on Jan 01 2012

city: Wuhan

first: Weiwei

last: Tie

state: Hubei Province

address: Shizishan Street, Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary:
Agrobacterium tumefaciens-mediated genetic transformation has been routinely used in rice for more than a decade. However, the transformation efficiency of the indica rice variety is still unsatisfactory and much lower than that of japonica cultivars. Further improvement on the transformation efficiency lies in the genetic manipulation of the plant itself, which requires a better understanding of the underlying process accounting for the susceptibility of plant cells to Agrobacterium infection as well as the identification of plant genes involved in the transformation process.
In order to investigate the related genes affecting the transformation efficiency of embryogenic calli of different rice cultivars, we used Affymetrix GeneChip® Rice Genome Array to measure the global gene expression profiling just before transformation and at four different time points after transformation (1 h, 6 h, 12 h, 24 h) in both japonica rice cultivar Nipponbare and indica rice cultivar Zhenshan 97.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: The mature embryo-derived embryogenic calli of Nipponbare (Nip) and Zhenshan 97 (ZS) were infected by Agrobacterium. Calli of Nip and ZS were sampled just before infection (0 h) and 1h, 6h, 12 h and 24h after infection, respectively. Three independent biological replications for each time point of the two varieties were used.   To avoid the influence of polymorphisms between the probe sequence on the array and the genomes of the varieties used, we used a genomic DNA (gDNA)-based probe-selection strategy based on the hybridization efficiency of gDNA from Nip and ZS with the PM oligonucleotide probes on the rice array. The genomic DNA of Nip and ZS were extracted and hybridized to the Affymetrix Rice Genome Arrays. Three biological replications per cultivar were performed.

first: Fei

last: Zhou

first: Hao

last: Chen

first: Lei

first: Weibo

last: Xie

first: Xianghua

last: Li

first: Yongjun

last: Lin


title: A single functional blast resistance gene Pi54 activates complex defense mechanism in Rice

status: Public on Dec 08 2011

city: New Delhi

first: Dr. Tilak

middle: Raj

last: Sharma

state: Delhi

address: 38 LBS Centre IARI Pusa Campus

department: Biotechnology

institute: National Research Centre on Plant Biotechnology

summary: To investigate the responses of resistance gene Pi54  at transcriptome level in  blast resistant transgenic rice line TP-Pi54 during infection by Magnaporthe oryzae, we studied the co-expression analysis using microarray  along with susceptible non-transgenic line Taipei 309 (TP). Suitable controls for both lines were used.  The comparative analysis of differentially expressed genes was conducted.

overall_design: Total RNA from  the leaves of  mock inoculated non transgenic line Taipei 309 (TP) and transgenic line (TP-Pi54) along with challenge inoculated plants were isolated at 72 hours post inoculation. The samples  were analyzed in two different biological replications (A and B) making total eight samples.

first: Santosh

last: Gupta

first: Amit

last: Rai

first: Duni

last: Chand

first: Shamsher

last: Kanwar

first: Nagendra

last: Singh

first: Tilak

middle: R


title: Expression data from PSARK::IPT and wildtype rice plants

status: Public on Oct 27 2011

city: Rehovot

first: Zvi

last: Peleg

address: P.O.Box 12

department: Inst. of Plant Sciences

country: Israel

institute: Hebrew University

summary: Transgenic rice plants expressing isopentenyltransferase (IPT), an enzyme that catalyzes the rate-limiting step in CK synthesis under the control of SARK, a maturation- and stress-inducible promoter. Increased CK production resulted in sink source alteration and enhanced drought tolerance of the transgenic plants.

overall_design: Flag leaf samples from well-watered (control) and water-stressed (3 days of withholding water) plants were collected for RNA extraction and hybridization on Affymetrix rice microarrays chip.

first: Eduardo

last: Blumwald


title: Expression data from rice after brown planthopper attack

first: Yubing

last: Wang

address: 300 fenglin road

institute: Institute of Plant Physiology and Ecology

summary:
The aim of this study was to analyze potential brown planthopper (BPH) resistant genes in Rathu Heenati (RHT) by Affymetrix whole rice genome array,BPH susceptible and resistant rice varieties of TN1（Taichung Native 1）as control. All the resistant related genes derived from RHT will be analyzed according to the SSR markers interval flanked on the chromosome 3, 4, 6 and 10. It will be benefit to the gene clone and marker assistant breeding for Bph3 gene in the near future.
We used microarrays to detail the global differential gene expression before and after brown planthopper attack in two different varieties, and identified distinct classes of high enriched genes induced by BPH or constituent in RHT

overall_design: The 2nd to 3rd instar nymphs of BPH were transferred to tillering stage seedings (10 BPH nymphs per plant) in a box covered with nylon-mesh. Stems of the rice plant infected by BPH were collected at 0h (T0), 8h (T8), 24h (T24) after BPH attack, total RNA were extracted for the microarray hybirdlization.

first: Xuexia

last: Miao


title: affy_meloidogyne_rice2-Oryza sativa genes expressed in the early compatible interaction with root-knot nematode

status: Public on Sep 25 2011

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary:
affy_meloidogyne_rice2 - affy_meloidogyne_rice2 - Plant-parasitic nematodes cause heavy economic losses to global agriculture. The root knot nematode, Meloidogyne incognita, is an obligate parasite that causes significant damage to a broad range of host plants. M. incognita infection to dicotyledous plants is extensively studied but it is also important to study their interaction with monocotyledous plants, in particular with cereals. In our growing conditions, as of day 6, histological studies revealed a profound rice tissue reorganisation around nematodes, notably characterized by the plant feeding site formation. We are investigating the molecular plant response to M. incognita by carrying out a global analysis of gene expression during gall formation in rice, using giant cell-enriched root tissues at this early stage (6dpi) 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 6 days before being inoculated with a 300 J2-stage juveniles M. incognita. 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 6 dai and each of them contained galls from 45 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

overall_design: 6 arrays - rice

first: Stephanie

last: Huguet

first: Stéphane

last: Bellafiore

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Amplified genes are not necessarily over expressed, they can be unchanged or down regulated in cervical cancer cell lines [SNP array data]

status: Public on Aug 01 2011

city: Mexico City

first: Jaime

last: Berumen

address: Dr. Balmis #148 Col. Doctores

department: Departamento de Medicina Experimental

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: Several copy number altered regions (CNA) have been identified in the genome of cervical cancer, especially amplifications of 3q and 5p. However, the contribution of those alterations to cervical carcinogenesis is still a matter of debate, since genome-wide, there is a lack of correlation between CNAs and gene expression. In this study, we investigated whether the CNAs in cell lines (CaLo, CasKi, HeLa, SiHa), at a gene-by-gene level, are related to changes in gene expression. On average 19.2% of the whole genome of cell lines had CNA. However, only 2.4% consisted of minimal recurrent regions (MRR), common to all cell lines. Whereas 3q had just some sparse common gains (13%), 5p was entirely duplicated recurrently. Genome-wide, only 11% of genes located in CNAs changed gene expression. In contrast, the rate increased over 3 fold times in MRRs. Chr 5p was confirmed entirely amplified by FISH. In spite of this, at most 32.9% of the explored genes in 5p (n=202) were de-regulated. In 3q, the rate was just 11.8%. Even in 3q26, which had five MRRs and 38.7% of SNPs was gained recurrently, the rate rose slightly to 13.6% (10 out of 73). Interestingly, up to 16% of de-regulated genes in 5p and 80% in 3q26 were down-regulated, suggesting additional factors are involved in gene repression. The de-regulated genes in 3q and 5p were found in clusters, suggesting local chromatin factors may also influence gene expression. In regions amplified discontinuously, the rate of down-regulated genes rose steadily as the number of amplified SNPs increased (p<0.01, Spearman's correlation). This suggests partial gene amplification as a mechanism of silencing gene expression. Additional genes were identified up- or down-regulated in 5p and 3q, which could be involved in cervical carcinogenesis, especially implicated in apoptosis. Those include CLPTM1L, AHRR, PDCD6 and DAP in 5p and TNFSF10 and ECT2 in 3q. Overall, the gene expression and copy number profiles suggest other factors, like epigenetic or chromatin domains, may influence gene expression within the entirely amplified genome segments. Further studies are needed to elucidate how these mechanisms regulate gene expression.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cell lines or peripheral blood samples. Copy number analysis of Affymetrix 100K SNP arrays was performed for 4 cervical cancer cell lines. DNA from 38 healty women were used as references for copy number inference.

first: Oscar

last: Vazquez-Mena


title: Genomic landscape of meningiomas: genotyping

status: Public on Oct 12 2011

city: Los Angeles

first: Stanley

last: Nelson

address: 695 Charles E. Young Drive South, Bldg Gonda, Rm 5554

department: Human Genetics

summary:
Meningiomas are one of the most common adult brain tumors.  For most patients, surgical excision is curative.  However, up to 20% recur.  Currently, the molecular determinants predicting recurrence and malignant transformation are lacking.  We performed global genetic and genomic analysis of 85 meningioma samples of various grades.
Copy number alterations were assessed by 100K SNP arrays and correlated with gene expression, proliferation indices, and clinical outcome.  In addition to chromosome 22q loss, which was detected in the majority of clinical samples, chromosome 18q and 6q loss significantly predicted recurrence and was associated with anaplastic histology.  Five "classes" of meningiomas were detected by gene expression analysis that correlated with copy number alterations, recurrence risk, and malignant histology.  These classes more accurately predicted tumor recurrence than Ki-67 index, the gold standard for determining risk of recurrence, and highlight substantial expression heterogeneity between meningiomas. These data offer the most complete description of the genomic landscape of meningiomas and provide a set of tools that could be used to more accurately stratify meningioma patients into prognostic risk groups.

overall_design: Tumor biopsies from 53 female and 32 male subjects with sporadic meningioma were identified from the UCLA Neuro-oncology Program Tissue Bank through institutional review board approved protocols.  57 tumors were designated "benign" WHO I, 20 tumors were "atypical" WHO II, and 8 were "anaplastic" WHO III. Affymetrix SNP arrays were performed according to the manufacturer's instructions on DNA extracted from flash frozen meningioma tumors.

first: Yohan

last: Lee


title: Human oocytes reprogram somatic cells to a pluripotent state

status: Public on Oct 06 2011

city: New York

first: Dieter

last: Egli

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

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


title: Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice

status: Public on Jul 20 2011

city: Montpellier

first: Yoan

last: Coudert

address: UM2 Place Eugène Bataillon

institute: Montpellier 2 University

summary: Expression data from rice crownrootless1 mutant and corresponding WT stem bases

overall_design: crl1 mutant and WT stem base transcriptomes were compared to identify genes whose expression is altered by crl1 mutation

first: Pascal

last: Gantet


title: SNP analysis of human induced pluripotent stem cells

status: Public on Sep 01 2011

city: Hinxton

first: Kosuke

last: Yusa

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: Wellcome Trust Sanger Institute

summary: Human induced pluripotent stem cells (hIPSCs) represent a unique opportunity for regenerative medicine since they offer the prospect of generating unlimited quantities of cells for autologous transplantation as a novel treatment for a broad range of disorders. However, the use of hIPSCs in the context of genetically inherited human disease will require correction of disease-causing mutations in a manner that is fully compatible with clinical applications. We analyzed hiPSC line and genetically modified derivatives using high-density SNP array to investigate genomic instability associated reprogramming and genetic modification.

overall_design: Primary iPSC lines derived from patients with alpha-1 antitrypsin deficiency were generated. This genetic disorder is caused by homozygous mutation (Glu342Lys) in the SERPINA1 gene. We carried out mutation correction by 2 steps: zinc-finger nuclease-stimuated gene targeting and piggyBac trasnsposon-mediated selection cassette elimination. Parental fibroblast lines, primary iPSC lines and homozygously targeted iPSC lines were subjected to SNP genotyping using Illumina CytoSNP-12 BeadChiP.


title: Genome-wide molecular characterisation of CNS PNET and Pineoblastoma

status: Public on Aug 22 2011

city: Nottingham

first: Suzanne

last: Miller

state: Nottinghamshire

address: Queen's Medical Centre

department: Human Development

institute: Children's Brain Tumour Research Centre

summary:
sPNETs are highly malignant embryonal brain tumours of poor prognosis. The underlying biology is poorly understood. To address this we therefore performed high resolution genetic analysis. 36 CNS PNETs and 8 PBs were analysed using the Affymetrix 100K and 500K Mapping Set to identify copy number imbalance at both the chromosome and gene level.

Keywords: Affymetrix 100K SNP array, Affymetrix 500K SNP arrays

overall_design: 36 CNS PNETs and 8 PBs with constitutional controls

first: Richard

last: Grundy


title: Differential expression for rice-gall midge interaction

status: Public on Nov 16 2011

city: Hyderabad

first: Nidhi

last: Rawat

address: Rajendranager

department: entomology

institute: Directorate of rice research

summary: We exposed Kavya rice seedlings to different gall midge biotypes, GMB1 and GMB4M, which exhibit incompatible and compatible interactions, respectively.

overall_design: Expression study in Kavya seedlings using pooled samples of stem meristematic tissues 24, 48, 96, and 120 hr after GMB1 and GMB4M infestation when compared with uninfested control. Three replicates each condition.

first: J

last: Bentur


title: Expression analysis of genes in the lamina joint of lc1 mutant compared with that of wild-type

status: Public on Jun 16 2011

city: Shanghai

first: Shuqing

last: Zhao

address: Fenglin 300

institute: SIPPE,CAS

summary: The angle of rice leaf inclination is an important agronomic trait and closely related to the yield and architecture of crops. Through genetic screening, a rice gain-of-function mutant leaf inclination1, lc1, was identified . Phenotypic analysis confirmed the exaggerated leaf angels of lc1 due to the stimulated cell elongation at the collar.In this series, we compare the transcriptome of zhonghua11 and lc1  collar.

overall_design: The lamina joint (1-cm long) of the flag leaves of lc1 and WT plants were collected and frozen in liquid nitrogen, which were then used for RNAs extraction. The obtained RNA samples were processed as recommended by Affymetrix, including RNA extraction, converting to double-stranded cDNA, and synthesis of biotin-labeled copy RNA. Fifteen micrograms of biotin-labeled copy RNA was purified and fragmented into 35- to 300-nucleotide fragments and then hybridized with a Rice genome array (Affymetrix). The hybridization was performed with two biological replicates for each sample. After hybridization, arrays were scanned using an Agilent GeneArray scanner (Affymetrix G2500A). Microarray data were normalized using the Affymetrix Microarray Suit program (version 5.0). The algorithm absolute call flag was set to indicate the reliability of the data points according to P (present), M (marginal), and A (absent). Significant differences for each gene between the WT and lc1 mutant plants were examined using the Wilcoxon rank test of the Affymetrix Microarray Suit program (P<0.01) and analysis of variance by fitting a mixed model in the MAANOVA package under R 1.8.0 for multiple testing (false discovery rate-corrected P<0.05). Genes with the consensus significant difference in two independent samples were selected and listed. Annotations for the selected probe set identification were rechecked at the Affymetrix website.