title: Transcript inhibition from limited starch degradation

summary: In starchless mutants of Arabidopsis, pgm, and wild type, Col0, there are small differences in transcript levels at the end of the day, but large differences at the end of the night. Many of the transcripts of genes involved in biosynthesis and growth are repressed in the pgm mutant (Thimm et al., 2004).  It is hypothesized that a transient depletion in sugars at the end of the night inhibits carbon utilization at the beginning of the day (Gibon et al., 2004).  In order to test if the same inhibition of transcripts involved in biosynthesis and growth also occurs in starch excess mutants of Arabidopsis, Affymetrix arrays will be generated for WT (Col0), and the following mutants: sex4-3 (Salk 102567), ptpkis2 (Salk 053285), and sex1-3 (Yu et al., 2001).  WT, sex4-3, and ptpkis2 plants were grown for 30 days and sex1-3 plants were grown for 36 days.  All plants were grown in a growth chamber with a 12 hour photoperiod, quantum flux  100 mol m-2s-1, relative humidity was at least 75%, and a constant temperature of 20oC.  Three leaves from 8 different plants of each genotype were harvested using a green safe lamp 0.5 hours before the lights came on in the morning and immediately frozen in LN2. Leaf material was powered using a mortar and pestle and RNA was extracted using a Purescript RNA isolation kit (Gentra Systems, MN, USA).  Samples were then treated with DNaseI (Invitrogen, CA, USA).

overall_design: 12 samples were used in this experiment.

first: Sean

last: Weise


title: Geographical Genomics of Human Leukocytes Gene Expression Variation

status: Public on Dec 01 2009

city: Raleigh

first: Youssef

last: Idaghdour

state: NC

address: South Gardner Hall

department: Genetics

country: USA

institute: NCSU

summary: Genome-wide association studies of transcript abundance in peripheral blood samples or derivative cell lines have demonstrated a preponderance of eSNP effects that, for the most part, involve regulatory polymorphisms in the differentially expressed gene.  Several of these highlight associations that contribute to a variety of disease conditions, but the question arises as to how the associations are affected by the environment.  Here we address the robustness of eSNP associations to environmental geography and population structure in a comparison of 194 Arab and Amazigh individuals from a city and two villages in southern Morocco.

overall_design: 194 individuals both men and women representing two ethnicities (Arabs and Amazighs) from three geographic locations (Agadir, Boutroch and Ighrem) and two lifestyles (Urban and Rural) were sampled under informed consent. Only healthy individuals aged between 18 and 50 were sampled. RNA from each was hybridized to an Illumina array. No technical replicates were performed in this study.

first: Youssaef

first: Greg

last: Gibson


title: Laser microdissection of Arabidopsis cells at the powdery mildew infection site

city: Berkeley

first: Mary

middle: C

last: Wildermuth

state: CA

address: 221 Koshland Hall MC3102

department: Plant and Microbial Biology

institute: University of California Berkeley

summary:
To elucidate host processes and components required for the sustained growth and reproduction of the obligate biotrophic fungus Golovinomyces orontii on Arabidopsis thaliana, laser microdissection was used to isolate cells at the site of infection at 5 days postinfection for downstream global Arabidopsis expression profiling. Site-specific profiling increased sensitivity dramatically, allowing us to identify specific host processes, process components, and their putative regulators hidden in previous whole-leaf global expression analyses. For example, 67 transcription factors exhibited altered expression at the powdery mildew (PM) infection site, with subsets of these playing known or inferred roles in photosynthesis, cold/dehydration responses, defense, auxin signaling, and the cell cycle. Using integrated informatics analyses, we constructed putative regulatory networks for a subset of these processes and provided strong support for host cell cycle modulation at the PM infection site. Further experimentation revealed induced host endoreduplication occurred exclusively at the infection site and led us to identify MYB3R4 as a transcriptional regulator of this process. Induced endoreduplication was abrogated in myb3r4 mutants, and G. orontii growth and reproduction were reduced. This suggests that, by increasing gene copy number, localized endoreduplication serves as a mechanism to meet the enhanced metabolic demands imposed by the fungus, which acquires all its nutrients from the plant host.
Keywords: endoreduplication, cell cycle, obligate biotroph

overall_design: Arabidopsis whole leaves from wild type Columbia-0 and enhanced disease susceptibility mutant eds16-1, a null isochorismate synthase 1 (At1g74710) mutant were harvested at 5 days after Golovinomyces orontii infection, microwave-fixed, paraffin-embedded and sectioned. Groups of epidermal and mesophyll cells (~20 cells/group) surrounding the G. orontii infected epidermal cell were cut using a Leica AS laser microdissection (LMD) system. In parallel, groups of epidermal and mesophyll cells were collected from uninfected leaves at 5 days from wild type Arabidopsis. LMD-isolated cells, whole leaf, whole leaf amplified and tissue scrape samples were used for RNA extraction and hybridization to Affymetrix Arabidopsis ATH1 microarrays.  Gene expression profiles were obtained for wild type from all samples and for ics1 mutant from LMD infected samples. The experiment includes 2 biological replicates.

first: Divya

last: Chandran


title: CD3+ T-cells of B-cell chronic lymphocytic leukemia

status: Public on Nov 25 2009

city: Essen

first: Lewin

last: Eisele

address: Hufelandstr. 55

department: Haematology

country: Germany

institute: University Hospital Essen

summary: Analysis of T-cells isolated from CD3+ T-cells of patients with B-cell chronic lymphocytic leukemia (B-CLL). In contrast to other types of cancers, the non-malignant T-cell compartment of B CLL patients is expanded. Results provide insights into the role of T-cells in B-CLL.

overall_design: Purified T-cells of B-CLL patients and normal donor T-cells were analyzed on microarrays to identify differentially expressed genes. The normal donor T-cell control data sets (n=8) have been previously  published in the GDS2908 record.

first: Joachim

middle: R

last: Göthert

first: Ludger

last: Klein-Hitpass

first: Stefanie

last: Weber

first: Anja

last: Führer

last: Sellmann

first: Alexander

last: Röth

first: Hanspeter

last: Pircher

first: Ulrich

last: Dührsen

first: Jan

last: Dürig


title: Expression data from overexpressers and mutants of TFs-gene LBD37 and LBD38 under different nitrogen regimes

status: Public on Nov 24 2009

city: Potsdam

first: Grit

last: Rubin

address: Am Mühlenberg 1

department: Stitt

institute: MPI-MP

summary:
Nitrogen (N) and nitrate (NO3-) per se regulate many aspects of plant metabolism, growth and development. N/NO3- also suppresses parts of secondary metabolism including anthocyanin synthesis. Molecular components for this repression are unknown. We report that three N/NO3--induced members of the LATERAL ORGAN BOUNDARY DOMAIN (LBD) gene family of transcription factors (LBD37, LBD38 and LBD39) act as negative regulators of anthocyanin biosynthesis in Arabidopsis (Arabidopsis thaliana). Over-expression of each of the three genes in the absence of N/NO3- strongly suppresses the key regulators of anthocyanin synthesis PAP1 and PAP2, genes in the anthocyanin-specific part of flavonoid synthesis, as well as cyanidin- but not quercetin- or kaempferol-glycoside production. Conversely, lbd37, lbd38 or lbd39 T-DNA insertion mutants accumulate anthocyanins when grown in N/NO3--sufficient conditions and show constitutive expression of anthocyanin biosynthetic genes. The LBD genes also repress many other known N-responsive genes including key genes required for NO3- uptake and assimilation, resulting in altered NO3- content, nitrate reductase activity/activation, protein, amino acid and starch levels, and N-related growth phenotypes. The results identify LBD37 and its two close homologs as novel repressers of anthocyanin biosynthesis and N-availability signals in general. They also show that besides being developmental regulators LBD genes fulfill roles in metabolic regulation.
We used microarrays to test whether LBD37 and LBD38 have a more widespread role in NO3-/N-regulation.

overall_design: 9-day old Arabidopsis seedlings were harvested for RNA extraction and hybridization on Affymetrix microarrays. Total RNA was prepared separately from three biological replicates of N-limited LBD37OX, LBD38OX and WT seedlings, and N-replete lbd37-1 mutant, lbd38 mutant and WT seedlings (18 samples).

first: Wolf-Rüdiger

last: Scheible


title: CYP3A5 Gene Expression is Associated with Early Recurrence of Non-small Cell Lung Cancer

city: Minneapolis

first: David

middle: A.

last: Potter

state: MN

address: 420 Delaware St. SE

department: Division of Hematology, Oncology and Transplantation

institute: University of Minnesota

summary:
Study to identify genes associated with NSCLC recurrence in patients not receiving adjuvant chemotherapy.
Purpose:  Recent clinical trials suggest improvement in survival with adjuvant chemotherapy in non-small cell lung cancer (NSCLC).  This study's aim is to identify genes associated with NSCLC recurrence in patients not receiving adjuvant chemotherapy. Experimental design: Banked NSCLC tumors of patients who underwent resection of stage Ia-IIIb disease were identified.  Patients were stratified into two groups: recurrent (R, n=11) or non-recurrent (NR, n=16) 2 years after surgery.  Microarray profiling and Cox multivariate analysis were performed. Conclusion:  Increased CYP3A5 gene expression correlates with NSCLC recurrence and promotes proliferation through mechanisms that may involve, in part, CYP3A5 epoxygenase activity.
Keywords: comparison of gene expression profiles for recurrent and non-recurrent cancer

first: Ranjana

last: Mitra

first: Clementina

last: Mesaros

first: Anjaiah

last: Srirangam

first: Ahmed

last: Mohiuddin

first: Todd

middle: P

last: Skaar

first: Beth

last: Juliar

first: Lang

last: Li

first: Sunil

last: Badve

first: Dafydd

last: Thomas

first: Oscar

last: Cummings

first: Jeanette

middle: N

last: McClintick

first: Howard

middle: J

last: Edenberg

first: Clement

last: McDonald

first: Ian

middle: A

last: Blair


title: Drosophila melanogaster spermatogenesis expression profile: mitotic, meiotic and post-meiotic cells

city: Chicago

first: Maria

middle: D

last: Vibranovski

state: IL

address: 1101 East 57th Street

department: Ecology and Evolution

institute: University of Chicago

summary:
We conducted a genome-wide expression analysis of wild-type males using three cell populations isolated from mitotic, meiotic and post-meiotic phases of spermatogenesis in Drosophila melanogaster. Our approach was to directly isolate testis regions enriched with RNAs from each of the three specific germline phases.
We used microarrays to detail the global gene expression profile in spermatogenesis and identified up- and down-regulated genes between two different spermatogenic phases in pairwise comparisons

overall_design: Cell types present at various stages of spermatogenesis are generally located in a gradient along the proximal-distal axis of the testis, however most are not exclusively restricted to any one geographic region. Cells enriched for mitotic, meiotic and post-meiotic phases were obtained by dissection of apical, proximal and distal regions of the testis, respectively

first: Hedibert

middle: F

last: Lopes

first: Timothy

middle: L

last: Karr

first: Manyuan

last: Long


title: Differential gene expression profiling from Arabidopsis thaliana wild type (Columbia-0) and lht1 mutant leaves

status: Public on Nov 20 2009

city: Saskatoon

first: Yangdou

last: Wei

state: SK

address: 112 Sceince Place

department: Biology

country: Canada

institute: University of Saskatchewan

summary: We found that amino acid transporter LHT1 was required for negatively regulating plant defence responses in addition to its physiological role in development and growth. In order to identify which defense pathways were involved in this process, we compared the expression profiles between wild type and lht1 mutant leaves without or with infection by Pseudomonas syringae pv. tomato DC3000 (Pst). In the lht1 mutant, except the changes in nitrogen metabolism-, cellular redox-, and photorespiration-associated gene expressions, the most drastic upregulations were found in the salicylic acid pathway-associated defense genes.

overall_design:
We used microarrays to detail the global profile of gene expression after knocking out the LHT1 gene and identified distinct classes of up- and down-regulated genes associated with the lht1 mutation.
The Arabidopsis plants grown for 3 weeks in short day condition, without or with 48hr pathogen infection, were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of leaves in order to better represent expression profiles. To that end, we hand-selected the leaves at the same stages (fully expanded) and mixed them together for each biological replicate.

first: Guosheng

last: Liu

first: Jitao

last: Zou


title: Transcriptome data from inflorescence stalks of intact A. thaliana plants after infection with A. tumefaciens

status: Public on Nov 19 2009

city: Wuerzburg

first: Rosalia

last: Deeken

address: Julius-von-Sachs-Platz 2

department: Botany I; Plant Molecular Physiology & Biophysics

institute: University of Wuerzburg, Julius-von-Sachs-Institute

summary:
The intention of these gene expression analysis was to study host responses to an infection with Agrobacterium tumefaciens at different stages of crown gall development. Therefore the transcriptome of infected inflorescence stalk tissue and mature crown galls of Arabidopsis thaliana (WS-2) was determined of three different time points. These were compared with the transcriptome of mock-infected inflorescence stalk tissue (reference) of the same age. The following time points were analyzed: (i) three hours post inoculation, before the T-DNA is integrated into the host genome (ii) six days after inoculation when the T-DNA is present in the nucleus and the oncogenes are expressed in the host cell, and (iii) 35 days after inoculation when a mature tumors has developed. For the three-hour- (3hpi) and six-day- time point (6dpi) plants were infected with the virulent strain C58, harboring a T-DNA, or with strain GV3101, containing a disarmed Ti-plasmid. This allows discrimination between signals which derive from the bacterial pathogen and the T-DNA encoded oncogenes.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Analysis of anther development by identifying downstream genes controlled by MS35/MYB26

status: Public on Dec 10 2009

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

summary: MALE STERILITY 35 (MS35/ MYB26) is a R2R3-type MYB transcription factor (Steiner-Large et al., 2003). MS35 is suggested to be a key regulator in the process of lignified secondary thickening in the anther endothecium which provides mechanical force for anther dehiscence (Dawson et al., 1999). The ms35 mutant bears non-dehiscent anthers and thus exhibits a male sterile phenotype. This microarray experiment aims to identify genes controlled by MS35 and thus establish the precise role MS35 plays during anther development. We have demonstrated that MS35 is expressed in the anther during pollen mitotic divisions. Comparisons of gene expression will be carried out between anthers from the Ler.gl (wild-type control) and ms35.gl (mutant) to identify genes with altered expression due to the ms35 mutation. The use of the gl marker will enable a prompt identification of the ms35 mutant amongst the segregating population. The wild-type control line was chosen to be Ler.gl which ensures that the changes of gene expression are not due to the gl mutation. Plants were grown in growth chambers at 22h of daylight (167 umol.m2.sec-1) at 24 C and 2h of night at 24 C. Developmental stages of anthers were defined by bud position and DAPI staining. As soon as the plants showed three fertile or sterile siliques, anther and filaments were collected from both lines at Pollen Mitosis I (PM I), bicellular, and PM II stage, separately. RNA was extracted using RNeasy Mini Kit (Qiagen, USA) and digested with DNase to eliminate genomic DNA contamination. The identified genes will be further analysed using bioinformatics and genomic (knockout) resources that are available for Arabidopsis.

first: Jie

last: Song


title: Arabidopsis thaliana six days after infection with Agrobacterium tumefaciens

summary: This study focuses on responses of the host plant to infection and transformation with Agrobacterium tumefaciens. Genome wide changes in gene expression were integrated with the alterations in metabolite levels six days after inoculation of agrobacteria. Plants were infected with the virulent strain C58, harboring a T-DNA, or with strain GV3101, containing a disarmed Ti-plasmid. This allows discrimination between signals which derive from the bacterial pathogen and the T-DNA encoded genes.

overall_design: The bases of Arabidopsis thaliana (WS-2) inflorescence stalks were wounded and immediately infected with Agrobacterium tumefaciens or mock-infected for six days. Stalks of intact plants were inoculated with the oncogenic strain C58 (C58 6dpi 1 to 3) or the non-virulent strain GV3101 (GV3101 6dpi 1 to 3) to provide conditions close to nature. The gene expression data of three independent experiments of infected material were compared with three non-infected samples (reference 6dpi 1 to 3). Differential gene expression was determined by applying the LIMMA package (Linear Models for Microarray Data; Smyth, G.K. (2004) Applic. Genet. Mol. Biol. 3, Article 3; http://www.bepress.com/sagmb/vol3/iss1/art3/).

first: Julia

last: Engelmann


title: Transcriptome of mature Arabidopsis thaliana crown galls

summary: This study describes physiological changes, morphological adaptations and the regulation of pathogen defense responses in Arabidopsis crown galls. Crown gall development was induced on intact plants under most natural conditions with Agrobacterium tumefaciens. Differential gene expression and the metabolite pattern was determined by comparing crown galls with mock-inoculated inflorescence stalk segments of the same age.

overall_design: The bases of Arabidopsis thaliana (WS-2) inflorescence stalks were wounded and immediately inoculated with Agrobacterium tumefaciens, strain C58, or mock-inoculated. Plants were cultivated for another 35 days under short day conditions (8 h illumination, 16 h darkness). Gene expression values of four independent experiments of treated material (C58 35dpi 1 to 4) were compared with four non-treated samples of the same age (reference 35dpi 1 to 4). Differential gene expression was analyzed by applying the LIMMA package (Linear Models for Microarray Data; Smyth, G.K. (2004) Applic. Genet. Mol. Biol. 3, Article 3; http://www.bepress.com/sagmb/vol3/iss1/art3/).

first: Tobias

last: Mueller


title: Arabidopsis thaliana mutant leaves treated with Pseudomonas syringae ES4326

status: Public on Nov 18 2009

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary:
In order to better understand the transcriptional networks triggered by pathogen inoculation, we monitored gene expression in leaves of mutant Arabidopsis plants, inoculated with Pseudomonas syringae ES4326 and wild type Col-0 plants grown in parallel.  Individual leaves were injected in the morning using a needle-less syringe with 10E5 cfu cm-2 PsmES4326 (suspended in 5 mM MgSO4).  For the wild type, leaves were also mock treated with 5 mM MgSO4.  Leaves were harvested 24 hours later.  Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius with 75% humidity and a 12 hour day length.

Keywords: Expression profilling by array

overall_design: 24 samples were used in this experiment

first: Raka

last: Mitra


title: Identification of early gibberellin (GA) responsive genes in Arabidopsis hypocotyls

summary:
The aim of the experiment was to identify early gibberellin (GA) responsive genes in the roots of an Arabidopsis GA deficient mutant.The GA deficient mutant used in this study is a transgenic line overexpressing the PcGA2ox1 gene. This mutant has an identical phenotype to ga1-3, but it does not require exogenous GA treatment for germination.Seeds were germinated on 1xMS + 1% (w/v) sucrose plates containing 0.7% gelrite, and grown under continous light. The plates were orientated vertically.After six days growth the plates were treated with or without 5uM GA4 for 0, 30, 60 and 180 minutes.Approximately 400 hypocotyls were harvested per timepoint using a razorblade and after excision the hypocotyls were frozen in liquid nitrogen giving a total of 7 experimental samples (1: untreated, 2: 30 mins GA4, 3: 30 mins untreated, 4: 60 mins GA4, 5: 60 mins untreated, 6: 180 mins GA4, 7: 180 mins untreated. Three biological replicates were performed giving a total of 21 root samples. Total RNA was isolated from the roots using the QIAGEN RNeasy method.

Keywords: Expression profiling by array

overall_design: 21 samples were used in this experiment

first: Anne

last: Gronlund


title: Molecular responses to external pH changes in roots of Arabidopsis thaliana

summary:
Plants live in soils that vary considerably, both spatially and over time, in terms of nutrient composition and pH. Consistently, plants have to recognize and adapt to these changes by altering their structure and metabolism. The goal of this array analysis is to characterize the global transcriptional response to external pH changes in roots, which to date is almost unexplored. Arabidopsis thaliana (Columbia-0) were grown in hydroponic cultures in basic nutrient solution. Two days before treatment the media was shifted to nutrient solution containing 5mM MES, pH 6. At the time of the treatment start (4 hours after light on) the plants were shifted to nutrient solutions of pH 4.5 and 6.0 (control). Root RNA samples from time point 1 and 8 hour after treatment start is used for array analyzes.

Keywords: Expression profilling by array

overall_design: 12 samples were used in this experiment

first: Ida

last: Lager


title: Arabidopsis thaliana three hours after infection with Agrobacterium tumefaciens

summary: This study focuses on responses of the host plant to infection with Agrobacterium tumefaciens. Genome wide changes in gene expression were integrated with the alterations in metabolite levels three hours after inoculation of agrobacteria. Plants were infected with the virulent strain C58, harboring a T-DNA, or with strain GV3101, containing a disarmed Ti-plasmid. This allows discrimination between signals which derive from the bacterial pathogen and the T-DNA encoded genes.

overall_design: The bases of Arabidopsis thaliana (WS-2) inflorescence stalks were wounded and immediately infected with Agrobacterium tumefaciens or mock-infected for three hours. Stalks of intact plants were inoculated with the oncogenic strain C58 (C58 3 hpi 1 to 6) or the non-virulent strain GV3101 (GV3101 3 hpi 1 to 3) to provide conditions close to nature. The gene expression data of three independent experiments of infected material were compared with six non-infected samples (reference 3 hpi 1 to 6). Differential gene expression was determined by applying the LIMMA package (Linear Models for Microarray Data; Smyth, G.K. (2004) Applic. Genet. Mol. Biol. 3, Article 3; http://www.bepress.com/sagmb/vol3/iss1/art3/).


title: Natural variation of auxin response

summary:
To assess natural variation of downstream auxin responses we subjected 7 different arabidopsis ecotypes to a time course of auxin treatments. 7d-old seedlings grown in liquid culture have been treated for 0, 30 min, 1h and 3h with 1 µM IAA.

Keywords: Expression profilling by array

overall_design: 83 samples were used in this experiment

first: Marcel

last: Quint


title: TAP-ORC2 and control ChIP experiments in Drosophila Kc167 cells

status: Public on Nov 10 2009

city: Durham

first: David

middle: M

last: MacAlpine

address: Box 3813 DUMC

department: Pharmacology and Cancer Biology

institute: Duke University Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary:
Expression data from Kc167 cells under normal conditions. Used to assess expression levels of genes with ORC bound at promoter.

Control experiments in support of our previous modencode submssion GSE17282.

overall_design:
Kc167 cells were harvested from log phase gorwth.  RNA extraction and hybridization on Affymetrix microarrays.

Chromatin immunoprecipitation with IgG against TAP-ORC2 or control cells.


title: Transcriptional profiling of leaf blades and petioles subjected to shade avoidance syndrome

status: Public on Nov 01 2009

city: Kitashirakawa, Sakyoku

first: Toshiaki

last: Kozuka

state: Kyoto

address: Oiwakecho

department: Depertment of Botany

country: Japan

institute: Kyoto University

summary: Plants grown under a canopy recognize changes in light quality and modify their growth patterns; this modification is known as shade avoidance syndrome. In leaves, leaf blade expansion is suppressed, whereas petiole elongation is promoted under the shade. However, the mechanisms that control these responses are largely unclear. Here, we demonstrated that both auxin and brassinosteroid (BR) are required for the normal leaf responses to shade. The microarray analysis of leaf blades and petioles treated with end-of-day far-red light (EODFR) revealed that almost half of the genes induced by the treatment in both parts were previously identified as auxin-responsive genes. Likewise, BR-responsive genes were overrepresented in the EODFR-induced genes. Hence, the auxin and BR responses were elevated by EODFR treatment in both leaf blades and petioles, although opposing growth responses were observed in these two parts. The analysis of the auxin-deficient doc1/big mutant and BR-deficient rot3/cyp90c1 mutant further indicates that auxin and BR were equally required for the normal petiole elongation response to the shade stimulus. In addition, the spotlight irradiation experiment revealed that phytochrome in leaf blades but not that in petioles regulated petiole elongation, which was probably mediated through regulation of the auxin/BR responses in petioles. On the basis of these findings, we conclude that auxin and BR cooperatively promote petiole elongation in response to the shade stimulus under the control of phytochrome in the leaf blade.

overall_design: The WT seedlings were grown for 19 days under continuous white light condition before experimental treatment with three light conditions. Seedlings were either maintained in white light for 2 h (WL), incubated in the dark condition for 2 h (D), or experienced a pulse irradiation of FR light before incubated in the dark condition for 2 h (FRD). Total RNAs were separately prepared from leaf blades and petioles after each light treatment. Three independent biological replicates were used.

first: Taku

last: Demura


title: Gene expression profiles of human osteosarcoma, set2

status: Public on Nov 04 2009

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

summary: Pulmonary metastasis continues to be the most common cause of death in osteosarcoma.  Indeed, the 5-year survival for newly diagnosed osteosarcoma patients has not significantly changed in over 20 years. Further understanding of the mechanisms of metastasis and resistance for this aggressive pediatric cancer is necessary. Pet dogs naturally develop osteosarcoma providing a novel opportunity to model metastasis development and progression. Given the accelerated biology of canine osteosarcoma, we hypothesized that a direct comparison of canine and pediatric osteosarcoma expression profiles may help identify novel metastasis-associated tumor targets that have been missed through the study of the human cancer alone.  Collectively, these data support the strong similarities between human and canine osteosarcoma and underline the opportunities provided by a comparative oncology approach as a means to improve our understanding of cancer biology and therapy.

overall_design: Profiles of human osteosarcoma, single channel design


title: Gene expression profiles of human osteosarcoma

overall_design: Profiles of human osteosarcoma and three normal tissues, single channel design

first: Melissa

last: Paoloni


title: Gene expression profiles of canine and human osteosarcoma

summary:
Pulmonary metastasis continues to be the most common cause of death in osteosarcoma.  Indeed, the 5-year survival for newly diagnosed osteosarcoma patients has not significantly changed in over 20 years. Further understanding of the mechanisms of metastasis and resistance for this aggressive pediatric cancer is necessary. Pet dogs naturally develop osteosarcoma providing a novel opportunity to model metastasis development and progression. Given the accelerated biology of canine osteosarcoma, we hypothesized that a direct comparison of canine and pediatric osteosarcoma expression profiles may help identify novel metastasis-associated tumor targets that have been missed through the study of the human cancer alone.  Collectively, these data support the strong similarities between human and canine osteosarcoma and underline the opportunities provided by a comparative oncology approach as a means to improve our understanding of cancer biology and therapy.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Canis lupus familiaris

platform_organism:
Homo sapiens
Canis lupus familiaris

overall_design: Two datasets consisting of canine osteosarcoma tumors, canine osteosarcoma cell lines, and three normal tissues and an analogous human dataset were used to define the similarity between human and canine osteosarcoma.  A third dataset, human osteosarcoma with outcome data, was then used to suggest that some of the differences between the canine and human osteosarcoma were, perhaps, related to survival.

last: Paolini

first: Chand

last: Khanna

first: Paul

middle: S

last: Meltzer

first: Timothy

last: Triche


title: Renal progenitor cell gene expression profiling

status: Public on Nov 03 2009

city: BARI

first: Fabio

last: Sallustio

address: P.zza G.Cesare

department: DETO

country: Italy

institute: University of Bari

summary:
Multipotent progenitor cells (MPs) have been observed in human kidneys and particularly in Bowman's capsule and proximal tubules. The kidney owns the ability to repair local damage and renal MPs may play a role in the regenerative processes. Microarray technology was applied to identify differentially expressed genes among resident MPs isolated from glomeruli and tubules of normal renal tissue, renal proximal tubular epithelial cells (RPTECs) and mesenchymal stem cells (MSCs).
The results of our analysis represent a starting point for further functional studies.
Keywords: cell type comparison

overall_design: This study includes three renal tissue samples which were processed to obtain  3 glomerular progenitor populations and 3 tubular ones. Three subcoltures of MSCs and RPTECs were included as well. The differences in gene expression patterns of the 4 cell types were found out.

first: Luca

last: De Benedictis

first: Francesco

last: Schena


title: Gene expression associated with lentiviral expression of PRAME in normal hematopoietic progenitors.

city: Seattle

first: Vivian

middle: G.

last: Oehler

state: WA

address: 1100 Fairview Ave. North, D4-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: To identify gene expression that distinguishes hematopoietic cells that express PRAME from those that do not, normal CD34+ cells with forced PRAME expression were compared to cells without PRAME expression in culture over time (days 4, 7, 14)  using Affymetrix HU-133A microarrays

overall_design: Normal CD34+ progenitor cells not expressing PRAME were transduced with either PRAME cDNA (no 3' utr) or a corresponding empty vector control by lentiviral vector infection.  Two replicates were performed for each condition (PRAME and control) at three experimental time points (days 4, 7, and 14 in culture).   A single-stranded linear amplification protocol was used to process total RNA (one microgram) for the microarrays. This protocols is described in detail in PMID 14706461.

middle: G

first: Katherine

last: Guthrie

first: Carrie

last: Cummings

first: Kathleen

last: Sabo

first: Brent

last: Wood

first: Ted

last: Gooley

first: Taimei

last: Yang

first: Mirjam

middle: T

last: Epping

first: Yaping

last: Shou

first: Era

last: Pogosova-Agadjanyan

first: Paula

last: Ladne

first: Derek

last: Stirewalt

first: Janis

last: Abkowitz

first: Jerald

last: Radich


title: Gene expression dissection of the circadian neuronal circuit of Drosophila identifies novel circadian genes

status: Public on Oct 31 2009

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

summary: Gene expression profiling of distinct members of a neuronal circuit has the potential to   identify candidate molecules and mechanisms that underlie the formation, organization   and function of the circuit. To this end, we report here the application of a novel method   to characterize RNAs from small numbers of specific Drosophila brain neurons, which   belong to the circadian circuit. We identified three different sets of mRNAs enriched in   different subclasses of clock neurons:  one is enriched in all clock neurons, a second is   enriched in PDF-positive clock neurons and a third is enriched in PDF-negative clock   neurons.  Moreover, we characterized 2 novel genes, Fer2 and dnocturnin, one from each   subgroup, which highlight subgroup-specific features and play important roles in   circadian rhythms. The methodology is a powerful tool not only to dissect the cellular   and molecular basis of circadian rhythms but also to molecularly characterize other   Drosophila neuronal circuits.

overall_design: Circadican related neuronal celltypes (Tim, Pdf) or general neurons (Elav) were labeled by GFP or YFP using specific Gal4 drivers. Expression of those celltypes were profiled after manual sorting of those GFP or YFP positive cells. 3 biological replicates were collected (except adult small pdf cells).

first: Emi

last: Nagoshi

first: Ela

last: Kula


title: Genome-wide analysis of gene expression in human oral tumor and negative margin oral tissue from matched patients.

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary: Analysis of gene expression levels from oral tumor and normal tissue. The purpose of this experiment was to compare profiles of gene expression between tumor and negative margin tissue  from matched patient samples.

overall_design: Total RNA obtained from excised patient tumor and negative margin oral tongue tissue samples.

first: David

middle: I

last: Smith

middle: W

first: Rebecca

last: Laborde

first: Xing

last: Xu

first: Jian

last: Gu

first: Christina

middle: B

last: Chung

first: Cinna

last: Monighetti

first: Sarah

last: Stanley

first: Kerry

last: Olsen

first: Jan

last: Kasperbauer

first: Eric

last: Moore

first: Adam

last: Broomer

first: Ruoying

last: Tan

first: Pius

last: Brzoska

first: Matthew

last: Muller

first: Yongming

last: Sun

first: Scott

last: Kuersten

first: Melissa

last: Barker

first: Francisco

last: DeLaVega


title: Effect of auxin signaling on flg22 response

city: Norwich

first: Daniel

last: MacLean

address: Colney Lane

department: Bioinformatics

institute: The Sainsbury Laboratory

summary:
Expression data after flg22 treatment on leaf discs in Col-0, 35S:AFB1 and 35S:miR393
We used microarrays to investigated the effect of auxin signaling on flg22 response pathway. We also compared if addition of auxin could simulated the 35S:AFB1 phenotype.

Keywords: stress response, disease state analysis

overall_design: Leaf discs were taken and let overnight in water to avoid the wound response. We then performed the treatment (flg22, flg22 from Agrobacterium tumefaciens, flg22 +NAA, NAA) to the media. The samples where harvested and freeze in liquid nitrogen at 0, 1 and 2h after treatment.

first: Alexandre

last: Robert-Seilaniantz

first: Dan

first: Jonathan

last: Jones


title: Expression from dark grown Arabidopsis Wild type (Wt, Col-o) and ein3-1eil1-1 (AT3G20770, AT2G27050) mutant seedlings

status: Public on Oct 20 2009

city: Peking

first: Shangwei

last: Zhong

address: YiHeYuan West Street

department: Life Science School

country: China

institute: Peking University, China

summary: Ethylene is a gaseous hormone that plays important roles in plant growth, development and stress responses. EIN3 was identified as a plant-specific transcription factor and its protein level rapidly increases upon ethylene treatment. We found that activation of EIN3 and EIN3-like 1 (EIL1) is both necessary and sufficient for ethylene-induced enhancement of seedling greening, as well as repression of the accumulation of protochlorophyllide, a phototoxic intermediate of chlorophyll synthesis. Therefore, comparation of the Wt and ein3-1eil1-1 mutant etiolated seedlings' gene expression at genome wide will be helpfull for us  to find the EIN3/EIL1 target genes in chlorophyll biosynthesis pathway. Here we used microarrays to detail the global gene expression under the regulation of EIN3/EIL1.Here we used microarrays to detail the global gene expression under the regulation of EIN3/EIL1.

overall_design: 4 days dark grown Wt and ein3-1eil1-1 (AT3G20770, AT2G27050) double mutant seedlings were collected for isolation RNA. Standard Affymetrix protocal and 25K Affymetrix chip (ATH1) were used for Microarry hybridization.

first: Fengying

last: An

first: Hongwei

last: Guo


title: Expression data from biopsies of Nasopharyngeal carcinoma (NPC) and non-malignant controls

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary:
Nasopharyngeal carcinoma (NPC) is a common cancer in southern China and South East Asia where more than 50,000 new cases are diagnosed each year.
We used microarrays to identify down or upregulated genes in NPC compared with non-malignant controls.

Keywords: Diseased versus control

overall_design: Snap frozen nasopharyngeal biopsies from 25 patients with histologically confirmed undifferentiated NPC were included in the microarray analysis. Controls were obtained from 3 patients with no evidence of malignancy.

first: LeeFah

last: Yap

first: Shikha

last: Bose

last: Fung

first: Jane

last: Starzcynski

first: Amyza

last: Saleh

first: Susan

last: Morgan

first: Christopher

last: Dawson

first: Marilyn

last: Chukwuma

first: Esther

last: Maina

first: Maike

last: Buettner

first: John

last: Arrand

first: Paul

middle: V

last: Lim

first: Lawrence

last: Young

first: SooHwang

last: Teo

first: Tatjana

last: Stankovic

first: Ciaran

last: Woodman

last: Murray


title: Overexpression of miR396

city: Rosario

first: Ramiro

last: Rodriguez

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

summary:
Transcript profile of 10 days-old seedlings over expressing miR396
Keywords: genetic modification

overall_design: 2 samples from 35S:miR396 plants vs 2 samples of wild type plants

middle: E

first: Martin

last: Mecchia

first: Detlef

last: Weigel

first: Javier

last: Palatnik


title: A Genomic Approach to Improve Prognosis and Predict Therapeutic Response in Chronic Lymphocytic Leukemia (Mayo_Ohio)

first: Daphne

middle: R

last: Friedman

address: 101 Science Drive, Room 2121, CIEMAS Bldg

summary:
Chronic lymphocytic leukemia (CLL) is a heterogeneous malignancy, characterized by a variable clinical course. While clinical and laboratory parameters are increasingly being used to refine prognosis, they do not accurately predict response to commonly used therapy.  We used gene expression profiling to generate and further refine prognostic and predictive markers.  Genomic signatures that reflect progressive disease and responses to chemotherapy or chemo-immunotherapy were created using cancer cell lines and patient leukemia samples.  We validated these signatures using independent clinical data from four separate cohorts representing a total of 301 CLL patients.  A prognostic genomic signature created from patient leukemic cell gene expression data coupled with clinical parameters could statistically differentiate patients with stable or progressive disease in the training dataset.  The progression signature was then validated in two independent datasets, demonstrating a capacity to accurately identify patients at risk for progressive disease.  In addition, two distinct genomic signatures that predict response to chlorambucil or pentostatin, cyclophosphamide, and rituximab were also generated and were shown to accurately distinguish responding and non-responding CLL patients.  Microarray analysis of CLL patients’ lymphocytes can be used to refine prognosis and predict response to different therapies.  These results have direct implications for standard and investigational therapeutics in CLL patients.
Keywords: Gene Expression Profiling of two phenotypic states (responders versus progressors)

overall_design: For the predictive genomic signature or response to pentostatin, cyclophosphamide, and rituximab, 20 CLL leukemia samples were used in the training set, and 20 CLL leukemia samples were used in the validation set

first: J-Brice

last: Weinberg

first: Neil

last: Kay

first: Diane

last: Jelinek

first: Renee

last: Tschumper

last: Byrd

first: Alicia

last: Volkheimer

first: Karen

last: Bond

first: Youwei

last: Chen

first: Ning

last: Jiang

first: Joseph

middle: O

last: Moore

first: Jon

middle: P

last: Gockerman

first: Louis

last: Diehl

first: Carlos

last: Decastro

first: Anil

last: Potti

last: Nevins


title: Microarray to determine gene expression changes in the DHR96 mutant

status: Public on Oct 16 2009

city: Salt Lake City

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah

summary: DHR96 is a Drosophila member of the CAR/PXR/LXR family of Nuclear receptors. To Identify potential target genes for the DHR96 nuclear receptor we used microarray analysis to identify genes that were mis-regulated relative to control animals in the DHR96 mutant.

overall_design: Total RNA was isolated from mature adult DHR96 mutant and genetically matched Canton S controls and subjected to affymetrix microarray analysis.

first: Matt

last: Sieber


title: B virus and HSV-1 Infected Human Foreskin Fibroblast (HFF) expression profiles

city: Atlanta

first: Julia

middle: K

last: Hilliard

state: GA

address: 50 Decatur St

institute: Georgia State University

summary:
The overall cellular gene expression patterns engaged as a result of B virus (E2490) and HSV-1 (MacIntyre) infection at 1h, 3h, and 5h post infection were analyzed. Differentially regulated immune responsive genes during the early infection stage were identified.
Keywords: B virus, HSV-1

overall_design: The variables tested were infection (Mock, BV, HSV-1) and time (1, 3, 5h). Samples were performed in biological duplicate.

first: Chih-Ling

last: Zao

first: Ali

middle: A

last: Pirani

first: Kim

last: Gernert


title: Immunopurified mRNA-ribosome complexes expose cell-type specific plasticity in response to hypoxia in Arabidopsis

status: Public on Oct 12 2009

city: Bayreuth

first: Angelika

last: Mustroph

address: Universitaetsstr. 30, NWI

department: Plant Physiology

institute: University Bayreuth

summary:
Plant organs are comprised of distinct cell types with unique assemblages of mRNAs. This is a collection of CEL files of mRNA profiles of the total steady-state mRNAs and polysomal mRNAs of distinct cell types of the whole root and shoot of 7-d-old Arabidopsis thaliana seedlings. The cell type specific mRNA populations are those present in ribosome-mRNA complexes. This sub-population of mRNAs was obtained by first establishing a collection of Arabidopsis lines that express a FLAG-epitope tagged ribosomal protein L18 (RPL18) directed by promoters expressed in specific cell types and regions. Thirteen different promoter:FLAG-RPL18 lines were used. The targeted cell types and promoters included root atrichoblast (non-hair) epidermal cells (pGL2), root endodermis (pSCR), root stelar xylem and pericycle (pWOL, pSHR), root phloem companion cells (phloem CC) (pSUC2, pSultr2;2), root proliferating cells (pRPL11C), root cortex meristematic cells (pCO2), root cortex elongation/maturation cells (pPEP), shoot mesophyll (pRBCS), shoot epidermis (pCER5), shoot guard cells (pKAT1), shoot bundle sheath (pSultr2;2), shoot phloem CC (pSUC2) and shoot trichomes (pGL2). A CaMV 35S promoter:FLAG-RPL18 line was used to obtain the polysomal mRNA of multiple cell types. The immunopurification of ribosome-mRNA complexes of specific cell types/regions was accomplished by the method described in Zanetti et al. (Plant Physiology, 138, 624-635; 2005). Hybridization of the immunopurified mRNAs to the Affymetrix ATH1 DNA microarray platform and subsequent data analysis permitted the identification of transcripts that are enriched or depleted in specific cell types/regions of roots and shoots. The dataset includes samples from cell types/regions from seedlings grown under control conditions and cell types/regions of seedlings exposed to low oxygen stress (hypoxia) for 2 h.

Keywords: cell-type specific expression, hypoxic stress, polysomal mRNA, abiotic stress, atrichoblasts, epidermis, cortex, endodermis, stele, phloem companion cells, guard cells, mesophyll

overall_design: 79 samples, 2 conditions (2 h hypoxia stress, 2 h non-stress), 2 RNA pools (Total mRNA and polysomal mRNA), 2 organs, 13 promoter lines, 2-4 replicates

last: Bailey-Serres


title: Immunopurified mRNA-ribosome complexes expose cell-type specific plasticity during hypoxia in Arabidopsis root tips

summary:
Plant organs are comprised of distinct cell types with unique assemblages of mRNAs. This is a collection of CEL files of mRNA profiles of the total steady-state mRNAs and polysomal mRNAs of distinct cell types of the root tip of 7-d-old Arabidopsis thaliana seedlings. The cell type specific mRNA populations are those present in ribosome-mRNA complexes. This sub-population of mRNAs was obtained by first establishing a collection of Arabidopsis lines that express a FLAG-epitope tagged ribosomal protein L18 (RPL18) directed by promoters expressed in specific cell types and regions. Four different promoter:FLAG-RPL18 lines were used. The targeted cell types and promoters included root endodermis (pSCR) and root stelar xylem and pericycle (pWOL, pSHR). A CaMV 35S promoter:FLAG-RPL18 line was used to obtain the polysomal mRNA of multiple cell types. The immunopurification of ribosome-mRNA complexes of specific cell types was accomplished by the method described in Zanetti et al. (Plant Physiology, 138, 624-635; 2005). Hybridization of the immunopurified mRNAs to the Affymetrix ATH1 DNA microarray platform and subsequent data analysis permitted the identification of transcripts that are enriched or depleted in specific cell types of root tips. The dataset includes samples from cell types from seedlings grown under control conditions and cell types of seedlings exposed to low oxygen stress (hypoxia) for 2 h.

Keywords: cell-type specific expression, hypoxic stress, polysomal mRNA, abiotic stress, endodermis, stele

overall_design: 20 samples, 2 conditions (2 h hypoxia stress, 2 h non-stress), 2 RNA pools (Total mRNA and polysomal mRNA), 4 promoter lines, 2 replicates

first: Maria

last: Zanetti

first: Hans

last: Holtan

first: Peter

last: Repetti


title: Gene expression in pif1pif3pif4pif5 mutant under dark or red light conditions

city: Albany

first: james

middle: m

last: tepperman

address: 800 Buchanan St.

department: Plant and Microbial Biology

institute: Plant Gene Expression Center/UC Berkeley

summary: Light initiates the seedling deetiolation transition by promoting major changes in gene expression mainly regulated by phytochrome (phy) photoreceptors. During the initial dark-to-light transition, phy photoactivation induces rapid changes in gene expression that eventually lead to the photomorphogenic development. Recent reports indicate that this process is achieved by phy-induced degradation of Phy-Interacting bHLH transcription Factors (PIFs) PIF1, PIF3 PIF4 and PIF5, which are partly redundant constitutive repressors of photomorphogenesis that accumulate in darkness. In order to test whether light/phy-regulated gene expression occurs through these PIFs, we have performed whole-genome expression analysis in the pif1pif3pif4pif5 quadruple mutant (pifq).

overall_design: Wild-type and pifq mutant seeds were plated on GM medium without sucrose at room temperature. During this procedure the seeds were routinely exposed to white light (WL) for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness, induced to germinate with a 5-min red pulse (Rp) (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before exposure to a terminal 5-min far red pulse (FRp) (58 μmol/m2/s) to suppress pseudo-dark effects. Seeds were then placed in either dark (D) or constant red light (Rc) (6.7 μmol/ m2/s) at 21°C for 45h (2d-old seedlings). Alternatively, 2d-old dark-grown seedlings were treated with 1h of red light (R1) (7.5 μmol/m2/s). Seed samples were harvested after stratification (5d stratified seeds).

first: Pablo

last: Leivar

first: James

last: Tepperman

middle: H

last: Quail


title: Immunopurified mRNA-ribosome complexes expose cell-type specific plasticity during hypoxia in Arabidopsis

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

overall_design: Refer to individual Series


title: Expression data from early anther

status: Public on Sep 23 2009

city: State College

first: Xuan

last: Ma

state: PA

address: Life Science Building 416

institute: penn state university

summary: We performed microarray experiments with RNAs from dissected immature anthers (stages 4-7) from wild-type, dyt1  and ams mutant plants, using the Affymetrix ATH1 chip.

overall_design: Anthers from Arabidopsis thaliana were selected at 4-7 stages of early development for RNA extraction and hybridization on Affymetrix microarrays.  Samples from two mutants and wild-type anther.

first: Baomin

last: Feng

first: Yiben

last: Peng


title: Seed maturation/ drying of altered Lys metabolism genotype

status: Public on Sep 20 2009

city: Rehovot

first: Ruthie

last: Ruthie

address: PO Box 26

department: Plant Science

country: Israel

institute: Weizmann Institute of Science

summary: In order to elucidate transcriptional and metabolic networks associated with Lys metabolism, we utilized developing seeds as a system in which Lys synthesis could be stimulated developmentally without application of chemicals and coupled this to a T-DNA insertion knockout mutation impaired in Lys catabolism. This seed-specific metabolic perturbation stimulated Lys accumulation starting from the initiation of storage reserve accumulation. Our results revealed that the response of seed metabolism to the inducible alteration of Lys metabolism was relatively minor, however, that which was observable operated in a modular manner. They also demonstrated that Lys metabolism is strongly associated with the operation of the TCA cycle, whilst largely disconnected from other metabolic networks. In contrast, the inducible alteration of Lys metabolism was strongly associated with gene networks, stimulating the expression of hundreds of genes controlling anabolic processes that are associated with plant performance and vigor, whilst suppressing a small number of genes associated with plant stress interactions. The most pronounced effect of the developmentally-inducible alteration of Lys metabolism was an induction of expression of a large set of genes encoding ribosomal proteins as well as genes encoding translation initiation and elongation factors, all of which are associated with protein synthesis. With respect to metabolic regulation, the inducible alteration of Lys metabolism was primarily associated with altered expression of genes belonging to networks of amino acids and sugar metabolism. The combined data are discussed within the context of network interactions both between and within metabolic and transcriptional control systems.

overall_design: Arabidopsis thaliana (WS) seeds of the WT and KD genotype (Zhu and Galili, 2003)were germinated on soil and grown  in the greenhouse (23oC). Flowers were marked and at given time intervals following flowering (14DAF to Dry ). Maturing siliques were collected, then seeds were dissected from  siliques . Mature seeds were collected at the end of the desiccation period and stored at 4ºC. Two repeats were collected from each time point. Three to five thousands seeds were harvested for each extraction.


title: Drosophila Divergence 20091001

status: Public on Oct 07 2009

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

institute: Reed College

summary: D. yakuba, D. simulans, and D. sechellia gDNA competitively hybridized against D. melanogaster to evaluate aCGH as a means to identify diverged orthologs.

sample_organism:
Drosophila melanogaster
Drosophila sechellia
Drosophila simulans
Drosophila yakuba

overall_design: 2 D. sechellia vs D. melanogaster hybs - with dye swap, 2 D. simulans vs D. melanogaster hybs with dye swap, and 8 D. yakuba vs D. melanogaster hybs with balanced dye swaps. D. yakuba vs. D. melanogaster were then analyzed in all 2,4,6,8 possible combinations that incorporated dye-swap to asses sources of variation.

first: Renn

middle: C

last: Suzy


title: Chloroplast polynucleotide phosphorylase null mutant (pnp1-1) and phosphate starvation

status: Public on Sep 12 2009

city: Ithaca

first: Chloe

last: Marchive

state: NY

address: Tower road

institute: Boyce Thompson Institute

summary: A prominent enzyme in organellar RNA metabolism is the exoribonuclease polynucleotide phosphorylase (PNPase), whose reversible activity is governed by the nucleotides diphosphate-inorganic phosphate ratio. In Chlamydomonas reinhardtii, PNPase regulates chloroplast transcript accumulation in response to phosphorus (P) starvation, and PNPase expression is repressed by the response regulator PSR1 under these conditions. Here, we investigated the role of PNPase in the Arabidopsis (Arabidopsis thaliana) P deprivation response by comparing wild-type and pnp mutant plants with respect to their morphology, metabolite profiles, and transcriptomes. We found that P-deprived pnp mutants develop aborted clusters of lateral roots, which are characterized by decreased auxin responsiveness and cell division, and exhibit cell death at the root tips. Electron microscopy revealed that the collapse of root organelles is enhanced in the pnp mutant under P deprivation and occurred with low frequency under P-replete conditions. Global analyses of metabolites and transcripts were carried out to understand the molecular bases of these altered P deprivation responses. We found that the pnp mutant expresses some elements of the deprivation response even when grown on a full nutrient medium, including altered transcript accumulation, although its total and inorganic P contents are not reduced. The pnp mutation also confers P status-independent responses, including but not limited to stress responses. Taken together, our data support the hypothesis that the activity of the chloroplast PNPase is involved in plant acclimation to P availability and that it may help maintain an appropriate balance of P metabolites even under normal growth conditions.

overall_design: For each timepoints (3h and one week), we compared WT and pnp1-1 on +P and on -P, so a total of eight conditions For each condition, three biological replicates of at least 4 seedlings (without roots) were analyzed.

first: Zhangjun

last: Fei

first: David

last: Stern


title: Analysis of chronic lymphocytic leukemia CLL cells and normal B cells

status: Public on Sep 10 2009

city: Los Angeles

first: Sanjai

last: Sharma

department: Hematology Oncology

institute: UCLA West LA VA Medical Center

summary:
We have analyzed 2 normal B cells isolated from peripheral blood and 5 CLL specimens with affy 133A microarray for expression.
We used microarrays to analyze gene expression in normal B cells and CLL cells.

overall_design: Hybridize RNA to the chip  for the above mentioned total 5 samples


title: Gene Expression of Circulating B Lymphocytes for Smoking-related Osteoporosis in Postmenopausal Females

status: Public on Sep 30 2009

city: Omaha

first: Peng

last: Xiao

state: NE

address: 601 N 30th ST Suite 6730

department: Biomedical Sciences & Osteoporosis Research Center

institute: Creighton University Medical Center

summary:
B cells produce important cytokines regulate bone metabolism. We comparison gene expression patterns of circulating B cells in blood from 20 postmenopausal female smokers with low or high bone mineral density (BMD): 10 low BMD vs. 10 high BMD.
In total 17 differentially expressed genes were identified with smoking-related osteoporosis.

Keywords: disease state analysis

overall_design: B cells were isolated from 70 ml of whole blood from each of 20 postmenopausal female smokers, 10 with high BMD and 10 with low BMD, using B cell positive isolation method (Dynabeads CD19,Pan B) from Invitrogen Life Technologies Dynal Biotech Inc,CA. Total RNA was extracted from B cells using Qiagen RNeasy Mini Kit.A total of 4ug totalRNA was used to produced targets for each subject according to standard Affymetrix procedures. Hybridization was made for each subject. Robust Multiarray Algorithm was used to normalize the expression data and smoking-related genes were analyzed using two-way ANOVA under mutiple-testing adjustment combined with our previous GEO data (GSE7429).

first: Xiang-Ding

last: Chen

first: Hong-Wen

last: Deng


title: Translational Changes Upon Dietary Restriction in Drosophila

status: Public on Oct 02 2009

city: La Jolla

first: Brian

middle: Matthew

last: Zid

state: California

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

summary: Analysis of the translational changes induced upon DR in male Drosophila.

overall_design: 1-2 day old flies were transferred onto 4% or 0.25% YE food for 6 days.  ~100 male flies were then ground and RNA was separated by size on a sucrose gradient and fractionated using a Teledyne density gradient fractionator and a polysome profile was produced by monitoring the abs at 252nm.  RNA was then prepared from the low (1-4 ribosomes bound) and high (5 or more ribosomes bound) translation fractions. A translational index was then calculated for each mRNA. The changes in translational index upon DR were then evaluated.  This was done in triplicate on individual biological replicates.

middle: M

first: Aric

last: Rogers

first: Pankaj

last: Kapahi


title: Expression data from normal and Fanconi anemia low density bone marrow cells

status: Public on Sep 15 2009

first: Grover

last: Bagby

address: 3181 SW Sam Jackson Park Rd.

department: Dept. of Medicine

institute: Oregon Health & Science University

summary:
Fanconi anemia (FA) is a rare inherited disease complicated by aplastic anemia.  There is evidence that hematopoietic stem cells have lost self replicative capacity and undergo apoptosis when exposed to inhibitory cytokines including interferon gamma and tumor necrosis factor-alpha.
We used gene expression microarrays to identify transcriptomal differences between bone marrow cells from normal volunteers and from children and adults with Fanconi anemia

overall_design: Fanconi anemia patients were identified using mitomycin C and/or diepoxybutane chromosomal breakage analysis.  Eleven normal volunteers and 21 FA patients were studied.  All FA patients with cytogenetic evidence of clonal evolution were excluded.  All FA patients with acute leukemia were excluded.  RNA was prepared from freshly obtained low density mononuclear cell fractions.

first: Jane

last: Yates


title: Gene expression comparison between Arabidopsis wild type (Col) and stomata mutant

status: Public on Sep 01 2009

city: Columbus

first: Zidian

last: Xie

state: OH

address: 1060 Carmack Rd.

department: Dept. of Plant Cellular and Molecular Biology

institute: The Ohio State University

summary: As the gate for gas exchange and water vapor, stomata play an essential role in plant development. It has been a long time that many research focus on how the opening and closing of stomata is controlled. Until recently, studies on how stomata are formed in Arabidopsis just emerge. With a cluster of guard cells in one stomate in flp-1/myb88 mutant, it will be great interest to understand how FLP/MYB88 control stomata development. By taking advantaging of microarray technology, we intend to study a set of genes regulated by FLP/MYB88, which will facilitate us to better explore the biological functions of FLP/MYB88 in stomata development, even in the biotic or abiotic stresses.

overall_design: By comparing the gene expression differences between the wild type and stomata mutant--flp-1/myb88, we are trying to see which genes' transcripts are affected in flp-1/myb88 mutant.

first: Dongmei

last: Li

first: Grotewold

last: Erich


title: AGO 1 IMMUNOPRECIPITATION MICROARRAYS

status: Public on Aug 31 2009

city: Ashburn

first: Ken

last: Sugino

address: 19700 Helix Dr

institute: Janelia Research Campus

summary: Little is known about the contribution of translational control to circadian rhythms. To address this issue and in particular translational control by microRNAs (miRNAs), we knocked down the miRNA biogenesis pathway in  Drosophila circadian tissues. In combination with an increase in circadian-mediated transcription, this severely affected Drosophila behavioral rhythms, indicating that miRNAs function in circadian timekeeping. To identify  miRNA–mRNA pairs important for this regulation, immunoprecipitation of AGO1 followed by microarray analysis identified mRNAs under miRNA-mediated control. They included three core clock mRNAs—clock (clk), vrille (vri), and clockworkorange (cwo). To identify miRNAs involved in circadian timekeeping, we exploited circadian cell-specific inhibition of the miRNA biogenesis pathway followed by tiling array analysis. This approach identified miRNAs expressed in fly head circadian tissue. Behavioral and molecular experiments show that one of these miRNAs, the developmental regulator bantam, has a role in the core circadian pacemaker. S2 cell biochemical experiments indicate that bantam regulates the translation of clk through an association with three target sites located within the clk 39 untranslated region (UTR). Moreover, clk transgenes harboring mutated bantam sites in their 39 UTRs rescue rhythms of clk mutant flies much less well than wild-type CLK transgenes.

overall_design: Ago IP immunoprecipitation was performed from fly heads collected at different circadian timpoints. For wild type samples 2 biological replicates were collected for each of the six analyzed timepoints from the head protein extract (INPUT) and AGO 1-immunoprecipitated samples (IP). Gene expression was analyzed from both samples by the use of oligonucleotide microarrays. The INPUT sample corresponding to ZT3 has only one replica.

first: Sebastian

last: Kadener


title: Molecular and functional characterization of FD-iPSC derived neural crest precursor cells

city: New York

first: Agnes

last: Viale

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary:
Global gene expression analysis of FD-iPSC and deribved neural crest cells

Here we report the derivation of patient specific Familial Dysautonomia-iPSCs and their directed differentiation into multiple cell types capable of modeling the tissue specific splicing defect in vitro.

overall_design:
Undifferentiated hESCs were exposed to control and drug treatments for 24 hours followed by mRNA expression analysis
Global gene expression analysis of FD-iPSC and derived neural crest cells

first: Gabsang

last: Lee

first: Lorenz

last: Studer


title: Gene expression profiling of bone marrow endothelial cells in patients with multiple myeloma

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary:
To determine a gene/molecular fingerprint of multiple myeloma (MM) endothelial cells (MMECs), also identifying some of the vascular mechanisms that govern the malignant progression from quiescent monoclonal gammopathy of undetermined significance (MGUS). A comparative gene expression profiling (GEP) was carried out on patient-derived MMECs and MGUS endothelial cells (MGECs) using the Affymetrix U133A Arrays. Expression of selective vascular markers were also validated by RT-PCR and immunoblotting analysis in primary cultures of ECs isolated from total bone marrow (BM)-mononuclear cells. Twenty-two genes were found differently expressed in MMECs compared to MGECs (with 14 down-regulated and 8 up-regulated), thus proving that molecular differences were maintained in vitro. Specific pathways analysis revealed transcriptional and protein expression changes for key regulators of extracellular matrix formation and bone remodeling, cell-adhesion, chemotaxis, angiogenesis, resistance to apoptosis, and cell-cycle regulation. Specifically, we focused on six of these genes (DIRAS3, SERPINF1, SRPX, BNIP3, IER3 and SEPW1), which were not previously functionally correlated to the overangiogenic phenotype of MMECs and disease activity. These data identified distinct EC gene expression profiles and some vascular phenotypes that could influence the remodeling of the BM-microenvironment in patients with active MM. A better understanding of the linkage between genetic and epigenetic events in MM tumor/ECs may contribute to the molecular classification of the disease, thereby identifying selective targets of more effective anti-vessel/stroma therapeutic strategies.

Keywords: Gene expression profiling, endothelial cells, Multiple Myeloma.

overall_design: This series of microarray experiments contains the gene expression profiles of five samples from HUVECs (Human Umbilical Vein Endothelial Cells) and five bone marrow ECs (endothelial cells) samples from newly diagnosed MGUS and MM patients, respectively. Centrifugation on Ficoll gradient of heparinized BM-aspirates was followed by polystyrene flask adherence to isolate stromal cells from plasma cells in suspension. Adherent stromal elements were first immunodepleted of macrophages and residual plasma cells with CD14 and CD38 monoclonal antibody (mAb)-coated flasks (mAbs were from Immunotech, Coulter, Marseilles, France), and then incubated with magnetic microbeads coated with Ulex europaeus-1 lectin. Freshly-isolated ECs were cultured in complete medium RPMI-1640 medium supplemented with 10% heat-inactivated FCS and 1% glutamine to allow cell spreading and growth. The purity and viability of EC cultures grown at least one passage (more than 97% viable cells) were assessed by fluorescence-activated cell sorting (FACS, FACS Canto II, Becton Dickinson, San Jose, CA) with double positivity for factor VIII-related antigen (FVIII-RA, a highly specific EC marker) and CD105 (or endoglyn, a molecule strongly expressed by ECs) as well as for CD14 and CD38 negativity. Analysis of mRNA transcripts for FVIII-RA, CD38, CD105 and IgH VDJ region was also performed by RT-PCR, and EC viability was assessed by trypan blue viable staining. HUVECs were purchased from Clonetics Biowhittaker (Walkersville, MD) and cultured in EGM-2MV media (Clonetics Biowhittaker). Five micrograms of total RNA was processed and, in accordance with the manufacturer's protocols, 15 micrograms of fragmented biotin-labelled cRNA were hybridized on GeneChip Human Genome U133A Arrays (Affymetrix Inc.). The arrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix). The images were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software and the probe level data converted to expression values using the Bioconductor function for the Robust Multi-Array average (RMA) procedure (Irizarry et al, 2003), in which perfect match intensities are background adjusted, quantile-quantile normalized and log2-transformed.

first: Roberto

last: Ria

first: Katia

last: Todoerti

first: Addolorata

last: Coluccia

first: Simona

last: Berardi

first: Annunziata

last: De Luisi

first: Fortunato

last: Morabito

first: Attilio

last: Guarini

first: Maria

last: Petrucci

first: Franco

last: Dammacco

first: Domenico

last: Ribatti

first: Antonino

last: Neri

first: Angelo

last: Vacca


title: Expression data from Drosophila Kc167 cell line

city: Sheffield

first: Martin

last: Zeidler

address: Western Bank

department: Dept of Biomedical Science

institute: University of Sheffield

summary: The consitutive activation of the JAK/STAT signalling cascade is reponsible for the majority of meyoproliferative disorders in humans, a disease that is also conserved in Drosophila. A gain-of-function mutation in the Drosophila JAK kinase leads to blood cell (haemocyte) overproliferation which eventually is manifested as black melanotic tumors. Haemocyte-like Drosophila Kc167 cells were used to identify downstream target genes of the JAK/STAT pathway which may be responsible for tumour generation and progression.

overall_design: Kc167 cells were activated with the principal JAK/STAT pathway ligand Unpaired (UPD) in a time course manner. To this end, for each transcript profiling condition and time point, biological duplicates were activated with UPD or Mock conditioned media for 30 min, and total RNA was extracted 2, 4 or 10h after initial addition of conditioned media. 12 samples were used for hybridization to the arrays.

first: Samira

last: Bina


title: CAMK1D amplification implicated in epithelial-mesenchymal transition in basal-like breast cancer (expr)

status: Public on Sep 08 2009

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

summary:
Title: CAMK1D amplification implicated in epithelial-mesenchymal transition in basal-like breast cancer

Summary: Breast cancer exhibits clinical and molecular heterogeneity, where expression-profiling studies have identified five major molecular subtypes.  The basal-like subtype, expressing basal epithelial markers and negative for estrogen receptor (ER), progesterone receptor (PR) and HER2, is associated with higher overall levels of DNA copy number alteration (CNA), specific CNAs (like gain on chromosome 10p), and poor prognosis.  Discovering the molecular genetic basis of tumor subtypes may provide new opportunities for therapy.  To identify the driver oncogene on 10p associated with basal-like tumors, we analyzed genomic profiles of 172 breast carcinomas.  The smallest shared region of gain spanned just seven genes at 10p13, including calcium/calmodulin-dependent protein kinase ID (CAMK1D), functioning in intracellular signaling but not previously linked to cancer.  By microarray, CAMK1D was overexpressed when amplified, and by immunohistochemistry exhibited elevated expression in invasive carcinomas compared to carcinoma in situ.  Engineered overexpression of CAMK1D in non-tumorigenic breast epithelial cells led to increased cell proliferation, and molecular and phenotypic alterations indicative of epithelial-mesenchymal transition (EMT), including loss of cell-cell adhesions and increased cell migration and invasion.  Our findings identify CAMK1D as a novel amplified oncogene linked to EMT in breast cancer, and as a potential therapeutic target with particular relevance to clinically unfavorable basal-like tumors.

overall_design:
Overall design: HEEBO oligonucleotide microarrays from the Stanford Functional Genomics Facility were used to perform gene expression profiling of four CAMK1D or control-transfected MCF10A breast epithelial cell line derivatives, in comparison to a universal RNA reference.  Gene set enrichment analysis was used to identify CAMK1D-assocatied gene sets.
Set of arrays that are part of repeated experiments
Cell Line: CAMK1D or vector transfected MCF10A breast epithelial cell line derivatives

Biological Replicate
Computed

first: Young

last: Kim


title: Heat shock response of til1-1 mutant plants

status: Public on Aug 28 2009

city: Taipei

first: Yee-yung

last: Charng

address: 128, Academia Rd. Sec. 2

department: Agric. Biotech. Res. Center

country: Taiwan

institute: Academia Sinica

summary: Several lipocalin genes from higher plants were shown to be responsive to both high and low temperature stresses and have been named as temperature-induced lipocalin (Til).  In this study, a reverse genetic approach was taken to elucidate the role of Arabidopsis Til1 (At5g58070) in thermotolerance.  We showed that Til1 proteins was constitutively expressed and increased significantly after heat shock treatment.  A T-DNA knockout line of Til1, designated as til1-1, could not produce Til1 and showed severe defects in basal and acquired thermotolerance.  Introducing a wild type copy of Til1 gene into til1-1 complemented the mutant phenotype.  Over-expression of Til1 in the wild type plant did not enhance thermotolerance.  Til1 is peripherally associated with plasma membrane, suggesting a regulatory or protective role of this protein in membrane function.  Transcriptomic analysis showed that the heat shock response in til1-1 was not altered as compared to the wild type plants.  The temperature threshold for heat shock protein induction was not affected by the level of Til1.  Ion leakage analysis revealed no significant difference in membrane stability between the wild type and til1-1 seedlings.  These results suggested that Til1 is not involved in regulating membrane fluidity or stability.  Nevertheless, the level of malondialdehyde was significantly higher in til1-1 than in the wild type after severe heat treatment.  The mutant plants were also more sensitive than the wild type to tert-butyl hydroperoxide, a reagent that induces lipid peroxidation.  Taken together, our data indicate that Til1 is an essential component for thermotolerance probably by acting against lipid peroxidation induced by severe heat stress.

overall_design: Total RNA was isolated from the seedlings of 7-d old wild-type and til1-1 mutant seedlings (a pool of about 100 plants per treatment in duplicates) harvested immediately after heat shock treatment. In this experiment, total 8 chips were used, 1 each for 2 biological replicates of the control and HS-treated samples for the wild type and mutant plants.

first: Wen-tzu

last: Chi

first: Raymond

last: Fung

first: Hsiang-chin

last: Liu

first: Ching-chi

last: Hsu


title: CAMK1D amplification implicated in epithelial-mesenchymal transition in basal-like breast cancer

type:
Expression profiling by array
Genome variation profiling by array


title: Effect of AtHRE1 and AtHRE2 overexpression in normoxia and hypoxia

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

institute: Sant'Anna School of Advanced Studies

summary: HRE1 and HRE2 are two ERF transcription factors induced by low oxygen. In this work we analyzed the effect of ectopic expression of HRE1 and HRE2 on the arabidopsis transcriptome in aerobic and hypoxic (1% O2) conditions. While HRE1 has a moderate effect on the expression of anaerobic genes under hypoxia, HRE2 does not affect them either under aerobic or hypoxic conditions.

overall_design:
We treated Arabidopsis seedling Col-0 (wt) and transgenic 35S::HRE1 and 35S::HRE2 , 7-day old, germinated in 12/12 light/dark photoperiod with:
-Control (23°C, dark, 21% O2, 4h).
-Hypoxia (23°C, dark, 1% O2, 4h).

Two biological replicates for each condition.

first: Francesco

last: Licausi

first: Joost

middle: T

last: van Dongen

first: Beatrice

last: Giuntoli

first: Giacomo

last: Novi

first: Santaniello

last: Antonietta

first: Peter

last: Geigenberger


title: Alterations of global gene expression by cigarette smoke

city: Washington

first: Jinguo

last: Chen

state: DC

address: 3800 Reservoir Road NW

department: Cancer Genetics and Epidemiology

institute: Georgetown University Lombardi Cancer Center

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

overall_design: Refer to individual Series


title: Expression data from healthy smokers

summary:
Little is known about alteration of the global gene expression by cigarette smoke (CS) and few biomarkers for smoking-related harm are available.
We used Affymetrix HG-U133A GeneChips to measure the transcriptomes in lymphocytes of 23 current healthy smokers. When heavy smokers were compared with light smokers, 311 genes demonstrated a significant difference in mRNA expression of their blood lymphocytes.

Keywords: dose response

overall_design: The goals of this study were to evaluate novel gene expression profiles and pathways affected by cigarette smoking, and to identify potential biomarkers for cigarette smoke exposure and harm. To this end,  we isolated the PBMC from 10 heavy and 13 light smokers, determined their gene expression profiles with Affymetrix microarray and analyzed their relationship with cigarette smoking.

middle: G

last: Shields


title: NCI-60 Cancer Cell Line

status: Public on Aug 26 2009

city: Charlottesville

first: Jae

last: Lee

department: Public Health Sciences

institute: University of Virginia

summary:
NCI-60 cancer cell lines were profiled with their genome-wide gene expression patterns using Affymetrix HG-U133A chips.
Keywords: NCI-60 cancer cell line expression profiling

overall_design: Total RNA sample of each of the NCI-60 cell lines was obtained before the treatment of any anticancer compound.


title: Probing gene misregulation in bodyguard, lacerata and fiddlehead mutants

status: Public on Oct 01 2009

city: Cologne

first: Derry

last: Voisin

address: Carl-von-Linne weg 10

department: Saedler

institute: Max Planck Institute for Breeding Research

summary:
Although bodyguard (bdg), lacerata (lcr) and fiddlehead (fdh) mutations affect three unrelated genes, they trigger similar effects, i.e. ectopic organ fusion, increase of cuticle permeability. After performing cutin and wax analyses on these Arabidopsis thaliana mutants, which did not coincide with the putative enzyme functions, we hypothesised that these mutations trigger a complex response which may be visible at the transcriptional level.
This analysis revealed that major changes in gene regulation are taking place in bodyguard (bdg), lacerata (lcr) and fiddlehead (fdh) mutants, massively affecting genes associated with lipid, cell wall and intracellular homeostasis but also with pathogen resistance.

overall_design: Plants carrying a stable allele of the bodyguard (bdg), lacerata (lcr) and fiddlehead (fdh) mutations, respectively, were grown on soil in parallel to wild type Columbia plants and under controlled growth conditions. Trays were periodically shifted to avoid any position effect and, to increase representativeness of the samples, each sample contains leaf tissue from 15 plants.

first: Heike

last: Stegemann

first: Alexander

last: Yephremov


title: Circadian analysis of miRNAs and their targets

first: Ken

last: Sugino

type: Expression profiling by genome tiling array


title: Unique Transcriptional Profile in Wrist Muscles From Cerebral Palsy Patients

city: San Diego

first: Lucas

middle: Robert

last: Smith

address: 3350 La Jolla Village Drive Mail Code 151

department: Bioengineering

summary:
Cerebral palsy is caused be an upper motor neuron lesion which casues spasticity as well as secondary effects on muscle .  Muscle from cerebral palsy patients is has been shown to be smaller, with more ECM and longer sarcomere lengths
We used microarrays to globally investigate the transcriptional adaptations of cerebral palsy muscle and research which muscle pathways are altered in the diseased state

Keywords: Disease state analysis

overall_design: Muscle biopsies were taken from children undergoing surgery which exposed wrist muscle extensors (n=8) and flexors (n=8) in both cerebral palsy patients (n=6) and control patients (n=2) for RNA extraction and hybridization to Affymetrix GeneChips .  Cerebral palsy patients were classified by a number of clinical scores.

first: Eva

last: Pontén

first: Samuel

last: Ward

first: Henry

last: Chambers

first: Shankar

last: Subramaniam

first: Richard

middle: L

last: Lieber


title: Muscle sample biopsies on hyperCKemical subjects

city: Milan

first: Marco

last: Crimi

address: Via F. Sforza, 35

department: Dept. of Neuroscience

institute: University of Milan

summary:
A cDNA microarray analysis of asymptomatic patients presenting moderately elevated serum Creatine Kinase levels
Keywords = Creatine Kinase
Keywords = Skeletal muscle
Keywords: ordered

last: Comi


title: Expression profiling of the Arabidopsis Mediator complex mutant pft1/med25 and wildtype infected with Fusarium oxysporum

status: Public on Aug 24 2009

city: St Lucia

first: Brendan

last: Kidd

state: QLD

address: 306 Carmody Road

department: Plant Industry

country: Australia

institute: CSIRO

summary: The Mediator complex is an evolutionary conserved multiprotein complex that plays an essential role in initiating and regulating transcription. Its function is to act as a universal adaptor between RNA Polymerase II and DNA-bound transcription factors to translate regulatory information from activators and repressors to the transcriptional machinery. We have found that the PFT1 gene (which encodes the MED25 subunit of the Mediator complex) is required for the uncompromised expression of both salicylic acid- and jasmonate-dependent defense genes as well as resistance to the leaf-infecting fungal pathogens, Alternaria brassicicola and Botrytis cinerea in Arabidopsis. Surprisingly, we found that the pft1/med25 mutant showed increased resistance to the root infecting pathogen Fusarium oxysporum and that this resistance was independent of classical defense genes. In addition, the over-expression of PFT1 led to increased susceptibility to F. oxysporum. Therefore, to explore this phenomenon further, we wished to use whole genome transcript profiling to identify which genes may be playing a role in pft1/med25-mediated resistance to F. oxysporum.

overall_design: We grew both WT and pft1/med25 plants for four weeks in soil. After four weeks we treated the plants by root-dipping in either water or a F. oxysporum spore suspension before replanting them back into soil. There were four independent replicates of each treatment and each replicate contained 20 plants each. The treatments were WT (mock): pft1 (mock): WT (infected): pft1 (infected). Each replicate (16 in total) was harvested after 48 hours and the resulting RNA was used for hybridization to an Affymetrix ATH1 chip.

middle: N

first: Cameron

middle: I

last: Edgar

first: Krish

last: Kumar

first: Peer

last: Schenk

first: Elizabeth

last: Aitken

first: John

last: Manners

first: Kemal

last: Kazan


title: Effect of deuterium oxide on Arabidopsis gene expression

status: Public on Sep 18 2009

city: St. Paul

first: William

middle: M.

last: Gray

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

summary:
2H2O has a long history as a protein or amino acid labeling techinique, and such labeling systems have proven effective for many different types of studies. A disadvantage of a 2H2O labeling system is that plant growth is inhibited as the percentage of deuterium in the medium increases. However the molecular effects of 2H2O on plant growth has not previoulsly been investigated.
To assist with the experimental design of proteomic 2H2O labeling studies, we used microarrays to determine the global effects of 2H2O on gene expression and to indentify genes which genes are effected by 2H2O treatment.

overall_design: RNA was prepared from Arabidopsis seedlings grown for seven days on either H2O control media or 30% 2H2O to examine the long-term effects of 2H2O treatment,and from seedlings shifted from H2O media to either 2H2O or H2O for 4 h to examine short-term effects on gene expression, and seedlings shifted from 2H2O to H2O for 4 h to examine recovery effects on gene expression.

first: XiaoYuan

last: Yang

first: Jerry

middle: D

last: Cohen


title: Gene expression profile in selenophosphate synthetase 1 (SPS1) knockdown Drosophila SL2 cell

status: Public on Aug 18 2009

city: Seoul

first: Byeong

middle: Jae

last: Lee

address: 599 Gwanak-ro, Gwanak-gu,

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary:
Selenophosphate, which is the active donor of selenium in selenocysteine (Sec) biosynthesis is synthesized from selenite and ATP by an enzyme designated as selenophosphate synthetase (SPS).There are two isoforms of SPS in higher eukaryotes,SPS1 and SPS2. Initially, both SPS1 and SPS2 were thought to be involved in selenophosphate synthesis. However, it was subsequently shown that only SPS2 catalyzes selenophosphate synthesis. Although SPS1 is an essential gene in Drosophila, its function has not been determined.
To identify transcriptional profile of SPS1 knockdown cells, which could offer valuable clues to identify molecular mechanism of SPS1, we introduced RNAi using its cognate double-stranded RNA into Drosophila SL2 cells, and then microarray analysis was carried out.

overall_design: In order to find primary or secondary target gene which is regulated by SPS1,Drosophila SL2 cells were harvested at day1, day3 and day5 after SPS1 knockown for RNA extraction and hybridization on Affymetrix microarrays.

first: Myoung-Sup

last: Shim

first: Jin-Young

last: Kim

first: Kwang-Hee

first: Hee-kyoug

last: Jung

first: Byeong-Jae


title: Germline genomic variations associated with childhood acute lymphoblastic leukemia

status: Public on Aug 16 2009

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: We identified germline single nucleotide polymorphisms (SNPs) associated with childhood acute lymphoblastic leukemia (ALL) and its subtypes.  Using the Affymetrix 500K Mapping array and publicly available genotypes, we identified 18 SNPs whose allele frequency differed (P<1x10-5) between a pediatric ALL population (n=317) and non-ALL controls (n=17,958).  Six of these SNPs differed (P≤0.05) in allele frequency among four ALL subtypes.  Two SNPs in ARID5B not only differed between ALL and non-ALL groups (rs10821936, P=1.4x10-15, odds ratio[OR]=1.91; rs10994982,  P=5.7x10-9, OR=1.62) but also distinguished B-hyperdiploid ALL from other subtypes (rs10821936, P=1.62 x10-5, OR=2.17; rs10994982, P=0.003, OR 1.72).  These ARID5B SNPs also distinguished B-hyperdiploid ALL from other subtypes in an independent validation cohort (n=124 children with ALL) (P=0.003 and P=0.0008, OR 2.45 and 2.86, respectively) and were associated with methotrexate accumulation and gene expression pattern in leukemic lymphoblasts.  We conclude that germline genomic variations affect susceptibility to and characteristics of specific ALL subtypes.

overall_design: We used microarrays to detail the global program of gene expression in primary leukemic blasts cells from children diagnosed with acute lymphoblastic leukemia.

first: Mary

middle: V

last: Relling


title: Toxicogenomic Comparison of TCDD and PCB 126 Responsiveness in Primary Human Hepatocytes

status: Public on Aug 19 2009

city: Niskayuna

first: Erik

last: Carlson

address: 1 Research Circle

institute: General Electric

summary: (Abstract) Toxicogenomics has great potential for enhancing our understanding of environmental chemical toxicity, hopefully leading to better-informed human health risk assessments. This study employed toxicogenomic technology to reveal species differences in response to two prototypical aryl hydrocarbon receptor (AHR) agonists, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and the polychlorinated biphenyl (PCB) congener PCB 126. Dose responses of primary cultures of rat and human hepatocytes were determined using species-specific microarrays sharing over 4,000 gene orthologs. Forty-seven human and 79 rat genes satisfied dose response criteria for both chemicals and were subjected to further analysis including the calculation of EC50 and the relative potency (REP) of PCB 126 for each gene. Only 5 responsive orthologous genes were shared between the two species, yet the geometric mean of the REPs for all rat and human modeled responsive genes were 0.06 (95% Confidence Interval (CI); 0.03-0.1) and 0.002 (95% CI; 0.001-0.005), respectively, suggesting broad species differences in the initial events that follow AHR activation but precede toxicity. This indicates that there are species differences in both the specific genes that responded and the agonist potency and relative potency for those genes. This observed insensitivity of human cells to PCB 126 is consistent with more traditional measurements of AHR activation (i.e., CYP1A1 enzyme activity) and suggests that the species difference in PCB 126 sensitivity is likely due to certain aspects of AHR function. That a species divergence also exists in this expanded AHR-regulated gene repertoire is a novel finding and should help when extrapolating animal data to humans.

overall_design: Primary hepatocyte cultures derived from 3 human donors were treated with vehicle (0.5% DMSO), TCDD (-14 to -6.5 log10 M) , or PCB 126 (-12 to -5 log10 M) for 48h. Total RNA was extracted and screened with HG-U133A microarrays for dose response.

first: Colin

last: McCulloch

first: Aruna

last: Koganti

first: Shirlean

last: Goodwin

first: Thomas

middle: R

last: Sutter

first: Jay

middle: B

last: Silkworth


title: Divergent Transcriptomic Responses to Aryl Hydrocarbon Receptor Agonists Between Rat and Human Primary Hepatocytes

middle: A

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: Phytochrome Interacting Factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary: Phytochromes are red/far red photosensors regulating numerous developmental programs in plants. Among them phytochrome A (phyA) is essential to enable seedling de-etiolation in continuous far-red (FR) light a condition mimicking the environment under a dense canopy. The ecological relevance of this response is demonstrated by the high mortality rate of phyA mutants germinating in deep vegetational shade. phyA signaling involves a direct interaction of the photoreceptor with members of the bHLH transcription factor family, PIF1 and PIF3 (Phytochrome Interacting Factor). Here we investigated the involvement of PIF4 and PIF5 in phyA signaling and found that they redundantly control de-etiolation in FR light. The pif4pif5 double mutant is hypersensitive to low fluence rates of FR light. This phenotype is dependent on FR light perception by phyA but does not rely on alterations of the phyA level. Our microarrays analysis shows that PIF4 and PIF5 are part of an inhibitory mechanism repressing the expression of some light-responsive genes in the dark and are also needed for full expression of several growth-related genes in the light. Unlike PIF1 and PIF3, PIF4 and PIF5 are not degraded in response to FR light indicating that they are light-regulated by a different mechanism. Our genetic analysis suggests that this is achieved through the sequestration of these PIFs by the closely related bHLH transcription factor HFR1 (long Hypocotyl in FR light).

overall_design: he pif4pif5 double mutant were compared to wild-type plants when kept in the dark or subjected to 1 or 24 hours of 0.5 or 5 µmol/m2/s far-red light respectively.

first: Séverine

last: Lorrain

first: Martine

last: Trevisan

first: Christian

last: Fankhauser


title: Expression data from Arabidopsis ppi2 mutants

status: Public on Aug 17 2009

city: pohang

first: Lee

last: Sookjin

address: san 31, POSTECH, hyojadong, namgu

department: POSTECH

institute: inhwan Hwang

summary:
Arabidopsis ppi2 plants have a T-DNA insertion in atToc159 and thus display a severe defect in protein import into chloroplasts. These mutants have an albino phenotype and also are seedling lethal.
We used microarrays to detail the induced genes in ppi2 plants compard to wild type plants.

overall_design: Arabidopsis plants, wild-type and ppi2 plants, were grown for 10 or 20 days, respectively, and total RNA was used for analysis.

first: Sookjin

first: Inhwan

last: Hwang


title: Waldenstrom's Macroglobulinemia patients: expression and aCGH data

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13400 E. Shea Blvd, MCCRB-300

institute: Mayo Clinic Arizona

summary:
Waldenström’s macroglobulinemia (WM) is a distinct clinicobiological entity defined as a B-cell neoplasm characterized by a lymphoplasmacytic infiltrate in the bone marrow and immunoglobulin M paraprotein production.  Cytogenetic analysis is limited by the difficulty in obtaining tumor metaphases and the genetic basis of the disease remains poorly defined.  We performed a comprehensive analysis in 42 WM patients by using high-resolution array-based comparative genomic hybridization with the Human Genome 244A microarray.  Overall, 83% of samples have chromosomal abnormalities, with a median of three abnormalities per patient (range 0 to 27).  The most common abnormality was 6q deletion (40%) and four non-overlapped minimal deleted regions (MDR) were identified.  Gain of 6p was the second most common abnormality (17%) and its presence was always concomitant with 6q loss.  An interstitial MDR was delineated at 13q14 including MIRN15A and MIRN16-1 in 10% of patients.  Other recurrent deletions were 7q22, 8p, 11q22-q23, 11q23-q24 and 17p11-p13 (7% each).  Copy gains were identified in chromosomes 18 (17%), 4 (12%), 3 (10%), 8q (10%) and Xq27.1-q28 (10%).  To note, we reported biallelic deletions and/or inactivating mutations with uniparental disomy in TRAF3 and TNFAIP3, two negative regulators of the NF-kB signaling pathway.  Furthermore, we confirmed the association between TRAF3 inactivation and increased transcriptional activity of NF-kB target genes.  Mutational activation of the NF-kB pathway, which is normally activated by ligand-receptor interactions within the bone marrow microenvironment, highlight its biologic importance, and suggest a therapeutic role for inhibitors of NF-KB pathway activation in the treatment of Waldenström’s macroglobulinemia.
Keywords: gene expression profiling; array comparative genomic hybridization

overall_design:
Expression data: Samples GSM318148-GSM318169.
We included 22 samples from WM patients. Tumor clone population was selected by CD19+ or concomitant CD19+ and CD138+ sorting.

aCGH data: Samples GSM318356-GSM318397.
We included samples from 42 WM patients. Tumor DNA samples were selected by CD19+ or concomitant CD19+ and CD138+ sorting.

first: Rafael

last: Fonseca


title: Differential gene expression in peripheral blood leukocytes as a function of estrogen

status: Public on Aug 10 2009

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary:
Gene expression profiling was carried out on peripheral blood mononuclear cells from 45 adult females. The primary research question is whether leukocyte gene expression differs in individuals with varying levels of estrogen signaling.

Keywords: Risk prediction

overall_design: Study includes adult females, 11 of whom were pre-menopausal, 12 of whom were post-menopausal, 10 of whom were post-menopausal and receiving aromatase inhibitors, and 12 of whom were receiving tamoxifen.